diff --git a/mkdocs.yml b/mkdocs.yml
index 28ba5d5b5a..0f5a1691fb 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -10,6 +10,7 @@ nav:
           - Data summary files: modality-agnostic-files/data-summary-files.md
           - Phenotypic and assessment data: modality-agnostic-files/phenotypic-and-assessment-data.md
           - Code: modality-agnostic-files/code.md
+          - Provenance: modality-agnostic-files/provenance.md
           - Events: modality-agnostic-files/events.md
       - Modality specific files:
           - Magnetic Resonance Imaging: modality-specific-files/magnetic-resonance-imaging-data.md
@@ -120,6 +121,9 @@ markdown_extensions:
         - name: tsvgz
           class: tsv
           format: !!python/name:bidsschematools.render.tsv.fence
+        - name: mermaid
+          class: mermaid
+          format: !!python/name:pymdownx.superfences.fence_code_format
   - admonition
   - pymdownx.details
 plugins:
diff --git a/src/introduction.md b/src/introduction.md
index 2a5a377fe7..f0070de928 100644
--- a/src/introduction.md
+++ b/src/introduction.md
@@ -192,6 +192,15 @@ For example:
     Scientific Data 12, (13841).
     [doi:10.1038/s41597-025-05543-2](https://doi.org/10.1038/s41597-025-05543-2)
 
+### Other extensions specific publications
+
+#### Provenance
+
+-   Rémi Adon, Stefan Appelhoff, Tibor Auer, Laurent Guillo, Yaroslav O Halchenko, David Keator, Christopher J Markiewicz, Thomas E Nichols, Jean-Baptiste Poline, Satrajit Ghosh, Camille Maumet (2021).
+    **BIDS-prov: a provenance framework for BIDS**.
+    OHBM 2021 - 25th Annual Meeting of the Organization for Human Brain Mapping, Jun 2021, Online, South Korea. pp.1-3
+    [https://inserm.hal.science/inserm-03478998v1](https://inserm.hal.science/inserm-03478998v1)
+
 ### Research Resource Identifier (RRID)
 
 BIDS has also a
diff --git a/src/metaschema.json b/src/metaschema.json
index e5d4c7b400..ea06b89fa0 100644
--- a/src/metaschema.json
+++ b/src/metaschema.json
@@ -359,6 +359,15 @@
                   },
                   "additionalProperties": false
                 },
+                "modality_agnostic": {
+                  "type": "object",
+                  "patternProperties": {
+                    "^[a-zA-Z0-9_]+$": {
+                      "$ref": "#/definitions/suffixRule"
+                    }
+                  },
+                  "additionalProperties": false
+                },
                 "tables": {
                   "type": "object",
                   "patternProperties": {
@@ -372,7 +381,7 @@
                   "additionalProperties": false
                 }
               },
-              "required": ["core", "tables"],
+              "required": ["core", "modality_agnostic", "tables"],
               "additionalProperties": false
             },
             "deriv": {
diff --git a/src/modality-agnostic-files/dataset-description.md b/src/modality-agnostic-files/dataset-description.md
index 79d75264c3..c4f45f259c 100644
--- a/src/modality-agnostic-files/dataset-description.md
+++ b/src/modality-agnostic-files/dataset-description.md
@@ -45,16 +45,9 @@ and a guide for using macros can be found at
    }
 ) }}
 
-Each object in the `GeneratedBy` array includes the following REQUIRED, RECOMMENDED
-and OPTIONAL keys:
-
-<!-- This block generates a table describing subfields within a metadata field.
-The definitions of these fields can be found in
-  src/schema/objects/metadata.yaml
-and a guide for using macros can be found at
- https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
--->
-{{ MACROS___make_subobject_table("metadata.GeneratedBy.items") }}
+!!! Note
+    See the [Provenance of a BIDS dataset](provenance.md#provenance-of-a-bids-dataset) section
+    for more information on how to describe provenance using the `GeneratedBy` field.
 
 Example:
 
@@ -107,8 +100,6 @@ Example:
 }
 ```
 
-### Derived dataset and pipeline description
-
 As for any BIDS dataset, a `dataset_description.json` file MUST be found at the
 top level of every derived dataset:
 `<dataset>/derivatives/<pipeline-name>/dataset_description.json`.
diff --git a/src/modality-agnostic-files/provenance-context.json b/src/modality-agnostic-files/provenance-context.json
new file mode 100644
index 0000000000..4947242e70
--- /dev/null
+++ b/src/modality-agnostic-files/provenance-context.json
@@ -0,0 +1,47 @@
+{
+    "@context": {
+        "prov" : "http://www.w3.org/ns/prov#",
+        "xsd": "http://www.w3.org/2001/XMLSchema#",
+        "RRID": "http://scicrunch.org/resolver/",
+        "Id": "@id",
+        "Type": "@type",
+        "Label": "http://www.w3.org/2000/01/rdf-schema#label",
+        "StartedAtTime" : {
+          "@id": "prov:startedAtTime",
+          "@type": "http://www.w3.org/2001/XMLSchema#dateTime"
+        },
+        "EndedAtTime" : {
+          "@id": "prov:endedAtTime",
+          "@type": "xsd:dateTime"
+        },
+        "GeneratedBy" : {
+          "@id": "prov:wasGeneratedBy",
+          "@type": "@id"
+        },
+        "AttributedTo" : {
+          "@id": "prov:wasAttributedTo",
+          "@type": "@id"
+        },
+        "AssociatedWith" : {
+          "@id": "prov:wasAssociatedWith",
+          "@type": "@id"
+        },
+        "InformedBy" : {
+          "@id": "prov:wasInformedBy",
+          "@type": "@id"
+        },
+        "Used" : {
+          "@id": "prov:used",
+          "@type": "@id"
+        },
+        "ActedOnBehalfOf" : {
+          "@id": "prov:actedOnBehalfOf",
+          "@type": "@id"
+        },
+        "Entities": "prov:Entity",
+        "Environments": "prov:Entity",
+        "Activities": "prov:Activity",
+        "Software": "prov:SoftwareAgent",
+        "Atlocation": "prov:atLocation"
+    }
+}
diff --git a/src/modality-agnostic-files/provenance.md b/src/modality-agnostic-files/provenance.md
new file mode 100644
index 0000000000..79f71bafc9
--- /dev/null
+++ b/src/modality-agnostic-files/provenance.md
@@ -0,0 +1,682 @@
+# Provenance
+
+Support for provenance was developed as a [BIDS Extension Proposal](../extensions.md#bids-extension-proposals).
+Please see [Citing BIDS](../introduction.md#citing-bids) on how to appropriately credit this extension when referring to it in the
+context of the academic literature.
+
+!!! bug
+    Change example links below once they are merged to bids-examples
+
+!!! example "Example datasets"
+
+    The following examples have been formatted using this specification
+    and can be used for practical guidance when curating a new dataset.
+
+    - [Provenance of DICOM to Nifti conversion with `dcm2niix`](https://github.com/bclenet/bids-examples/tree/BEP028_dcm2niix/provenance_dcm2niix) - [Associated Pull Request #494](https://github.com/bids-standard/bids-examples/pull/494)
+    - [Provenance of DICOM to Nifti conversion with `heudiconv`](https://github.com/bclenet/bids-examples/tree/BEP028_heudiconv/provenance_heudiconv) - [Associated Pull Request #496](https://github.com/bids-standard/bids-examples/pull/496)
+    - [Provenance of fMRI preprocessing with `SPM`](https://github.com/bclenet/bids-examples/tree/BEP028_spm/provenance_spm) - [Associated Pull Request #497](https://github.com/bids-standard/bids-examples/pull/497)
+    - [Provenance of fMRI preprocessing with `fMRIPrep`](https://github.com/bclenet/bids-examples/tree/BEP028_fmriprep/provenance_fmriprep) - [Associated Pull Request#502](https://github.com/bids-standard/bids-examples/pull/502)
+
+    Further datasets are available from
+    the [BIDS examples repository](https://bids-website.readthedocs.io/en/latest/datasets/examples.html#provenance).
+
+## Overview
+
+This part of the BIDS specification is aimed at describing the provenance of a BIDS dataset.
+
+This description is retrospective: it describes a set of steps that were executed in order to obtain the dataset.
+
+!!! note
+    This is different from prospective provenance that focuses describing workflows that may be run on a dataset.
+
+This description is based on the [W3C Prov](https://www.w3.org/TR/2013/REC-prov-o-20130430/) standard.
+
+### General principles
+
+Provenance information SHOULD be included in a BIDS dataset when possible.
+
+If provenance information is included, it MUST be described using the conventions detailed by this specification.
+
+Provenance information reflects the provenance of a full dataset and/or of specific files at any level of the BIDS hierarchy.
+
+Provenance information SHOULD not include human subject identifying data.
+
+### Key concepts
+
+Provenance information is encoded using metadata fields.
+
+For the most part, this metadata consists of **provenance objects** of 4 types:
+
+-   **Activities**: transformations that have been applied to data.
+-   **Entities**: input or output data for activities.
+-   **Software**: software packages used to compute the activities.
+-   **Environments**: software environments in which activities were performed.
+
+!!! example "Minimal provenance example"
+
+    ```mermaid
+    flowchart BT
+        B[Brain extraction] -->|wasAssociatedWith| S{FSL<br>}
+        B -->|used| T1([sub-001_T1w.nii])
+        B -->|used| L((Linux))
+        T1p([sub-001_T1w_preproc.nii]) -->|wasGeneratedBy| B
+    ```
+
+    In this example, a brain extraction algorithm was applied on a T1-weighted image:
+
+    - *sub-001_T1w.nii* is the original T1-weighted image;
+    - *sub-001_T1w_preproc.nii* is the skull striped image;
+    - the *"Brain extraction"* activity was performed using the *FSL* software within a *Linux* software environment.
+
+Provenance objects are described as JSON objects in BIDS. They are stored inside **provenance files** (see [Provenance files](#provenance-files)).
+
+Additionally, metadata of entities can be stored as regular BIDS metadata inside:
+
+-   sidecar JSON files (see [Provenance of a BIDS file](#provenance-of-a-bids-file));
+-   `dataset_description.json` files (see [Provenance of a BIDS dataset](#provenance-of-a-bids-dataset)).
+
+## Provenance files
+
+Template:
+
+```text
+prov/
+    [<subdir>/]
+        prov-<label>_act.json
+        prov-<label>_ent.json
+        prov-<label>_env.json
+        prov-<label>_soft.json
+```
+
+!!! note
+    The `prov` BIDS entity allows to group related provenance files, using an arbitrary value for `<label>`. A subdirectory MAY be used to organize provenance files, using an arbitrary value for `<subdir>`.
+
+The following suffixes specify the contents of provenance files.
+
+<!--
+This block generates a suffix table.
+The definitions of these fields can be found in
+  src/schema/objects/suffixes
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_suffix_table(
+      ["act", "ent", "env", "soft"]
+   )
+}}
+
+!!! example "Example of organization for provenance files"
+    ```
+    prov/
+    ├─ preprocspm/
+    │  ├─ prov-preprocspm1_act.json
+    │  ├─ prov-preprocspm1_ent.json
+    │  ├─ prov-preprocspm2_act.json
+    │  └─ prov-preprocspm2_ent.json
+    ├─ prov-preprocfsl_act.json
+    ├─ prov-preprocfsl_ent.json
+    ├─ prov-preprocfsl_env.json
+    ├─ prov-preprocfsl_soft.json
+    └─ ...
+    ```
+
+### Activities
+
+Each `prov/[<subdir>/]prov-<label>_act.json` file is a JSON file describing activities.
+
+Each file MUST include the following key:
+
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_metadata_table(
+   {
+      "Activities": "REQUIRED"
+   }
+) }}
+
+Each object in the `Activities` array includes the following keys:
+
+<!-- This block generates a table describing subfields within a metadata field.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_subobject_table("metadata.Activities.items") }}
+
+!!! example "Example: a provenance object in a `prov/[<subdir>/]prov-<label>_act.json` file"
+    ```JSON
+    {
+        "Activities": [
+            {
+                "Id": "bids::prov/#conversion-00f3a18f",
+                "Label": "Dicom to Nifti conversion",
+                "Command": "dcm2niix -o . -f sub-%i/anat/sub-%i_T1w sourcedata/dicoms",
+                "AssociatedWith": "bids::prov/#dcm2niix-khhkm7u1",
+                "Used": [
+                    "bids::prov/#fedora-uldfv058",
+                    "bids::sourcedata/dicoms"
+                ],
+                "StartedAtTime": "2025-03-13T10:26:00",
+                "EndedAtTime": "2025-03-13T10:26:05"
+            }
+        ]
+    }
+    ```
+    This snippet is similar to Activities described in the [DICOM to Nifti conversion with `dcm2niix` example](https://github.com/bclenet/bids-examples/tree/BEP028_dcm2niix/provenance_dcm2niix).
+
+### Entities
+
+Each `prov/[<subdir>/]prov-<label>_ent.json` file is a JSON file describing entities.
+
+!!! warning
+    These files MUST not contain entities describing data files that are available in the dataset. Use sidecar JSON files instead for this purpose (see [Provenance of a BIDS file](#provenance-of-a-bids-file)).
+
+    These files MUST not contain entities describing the current dataset. Use `dataset_description.json` files instead for this purpose (see [Provenance of a BIDS dataset](#provenance-of-a-bids-dataset)).
+
+Inside provenance files, entity objects MAY describe:
+
+-   files or data that are located in another dataset;
+-   files or data that were deleted during the creation of the dataset;
+-   different versions of the same files or data that were modified during the creation of the dataset;
+-   files or data that are external to the dataset (for example templates shipped with software packages or environments);
+-   any other files or data that do not match the previously listed cases, as long as the entity cannot be described in a sidecar JSON or in `dataset_description.json`.
+
+Each file MUST include the following key:
+
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_metadata_table(
+   {
+      "Entities": "REQUIRED"
+   }
+) }}
+
+Each object in the `Entities` array includes the following keys:
+
+<!-- This block generates a table describing subfields within a metadata field.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_subobject_table("metadata.Entities.items") }}
+
+!!! example "Example: a provenance object in a `prov/[<subdir>/]prov-<label>_ent.json` file"
+    ```JSON
+    {
+        "Entities": [
+            {
+                "Id": "bids::sub-01/func/sub-01_task-tonecounting_bold.nii",
+                "Label": "sub-01_task-tonecounting_bold.nii",
+                "AtLocation": "sub-01/func/sub-01_task-tonecounting_bold.nii",
+                "GeneratedBy": "bids::prov#realign-acea8093",
+                "Digest": {
+                    "sha256": "a4e801438b9c36df010309c94fc4ef8b07d95e7d9cb2edb8c212a5e5efc78d90"
+                }
+            }
+        ]
+    }
+    ```
+    This is a snippet from the [fMRI preprocessing with `SPM` example](https://github.com/bclenet/bids-examples/tree/BEP028_spm/provenance_spm)
+
+### Software
+
+Each `prov/[<subdir>/]prov-<label>_soft.json` file is a JSON file describing software.
+
+Each file MUST include the following key:
+
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_metadata_table(
+   {
+      "Software": "REQUIRED"
+   }
+) }}
+
+Each object in the `Software` array includes the following keys:
+
+<!-- This block generates a table describing subfields within a metadata field.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_subobject_table("metadata.Software.items") }}
+
+!!! example "Example: a provenance object in a `prov/[<subdir>/]prov-<label>_soft.json` file"
+    ```JSON
+    {
+        "Software": [
+            {
+                "Id": "bids::prov/#dcm2niix-khhkm7u1",
+                "AltIdentifier": "RRID:SCR_023517",
+                "Label": "dcm2niix",
+                "Version": "v1.0.20220720"
+            }
+        ]
+    }
+    ```
+    This is a snippet from the [DICOM to Nifti conversion with `dcm2niix` example](https://github.com/bclenet/bids-examples/tree/BEP028_dcm2niix/provenance_dcm2niix)
+
+### Environments
+
+Each `prov/[<subdir>/]prov-<label>_env.json` file is a JSON file describing environments.
+
+Each file MUST include the following key:
+
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_metadata_table(
+   {
+      "Environments": "REQUIRED"
+   }
+) }}
+
+Each object in the `Environments` array includes the following keys:
+
+<!-- This block generates a table describing subfields within a metadata field.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_subobject_table("metadata.Environments.items") }}
+
+!!! example "Example: a provenance object in a `prov/[<subdir>/]prov-<label>_env.json` file"
+    ```JSON
+    {
+        "Environments": [
+            {
+                "Id": "bids::prov/#fedora-uldfv058",
+                "Label": "Fedora release 36 (Thirty Six)",
+                "OperatingSystem": "GNU/Linux 6.2.15-100.fc36.x86_64"
+            }
+        ]
+    }
+    ```
+    This is a snippet from the [DICOM to Nifti conversion with `dcm2niix` example](https://github.com/bclenet/bids-examples/tree/BEP028_dcm2niix/provenance_dcm2niix)
+
+## Provenance of a BIDS file
+
+Metadata of an entity describing a BIDS file MAY be stored inside its sidecar JSON.
+
+Any sidecar JSON file MAY include the following keys:
+
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_metadata_table(
+   {
+      "GeneratedById": "OPTIONAL",
+      "SidecarGeneratedBy": "OPTIONAL",
+      "Digest": "OPTIONAL",
+      "EntityType": "OPTIONAL"
+   }
+) }}
+
+!!! example "Example of metadata in a sidecar JSON file"
+    ```JSON
+    {
+        "GeneratedBy": "bids::prov#conversion-00f3a18f",
+        "SidecarGeneratedBy": [
+            "bids::prov#preparation-conversion-1xkhm1ft",
+            "bids::prov#conversion-00f3a18f"
+        ],
+        "Digest": {
+            "sha256": "66eeafb465559148e0222d4079558a8354eb09b9efabcc47cd5b8af6eed51907"
+        }
+    }
+    ```
+    This snippet is similar to fields described in [DICOM to Nifti conversion with `heudiconv` example](https://github.com/bclenet/bids-examples/tree/BEP028_heudiconv/provenance_heudiconv).
+
+## Provenance of a BIDS dataset
+
+Metadata of an entity describing a BIDS dataset (raw, derivative, or study) MAY be stored inside its `dataset_description.json` file.
+
+This metadata describes the provenance of the whole dataset.
+
+The `dataset_description.json` file of a **BIDS raw dataset** or **BIDS study dataset** MAY include the following key to describe provenance.
+
+The `dataset_description.json` file of a **BIDS derivative dataset** MUST include the following key to describe provenance.
+
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_metadata_table(
+   {
+      "GeneratedBy": "RECOMMENDED for BIDS raw datasets and BIDS study datasets, REQUIRED for BIDS derivative datasets"
+   }
+) }}
+
+The `GeneratedBy` field MAY contain either of the following values:
+
+-   Identifier(s) of the activity (one or more) responsible for the creation of the dataset (see the [Description using provenance objects](#description-using-provenance-objects) section).
+-   A description of pipelines or processes responsible for the creation of the dataset (see the [Description of pipelines or processes](#description-of-pipelines-or-processes) section).
+
+### Description using provenance objects
+
+This section details a way to describe the provenance of a dataset using provenance objects, providing `GeneratedBy` with the identifier(s) of the activity (one or more) responsible for the creation of the dataset.
+
+Related activities MUST be described inside the dataset (see the [Activities](#activities) section).
+
+!!! example "Example of `GeneratedBy` contents in a `dataset_description.json`"
+    ```JSON
+    {
+        "GeneratedBy": "bids::prov#preprocessing-xMpFqB5q"
+    }
+    ```
+    This is a snippet from the [fMRI preprocessing with `fMRIPrep` example](https://github.com/bclenet/bids-examples/tree/BEP028_fmriprep/provenance_fmriprep).
+
+### Description of processes or pipelines
+
+This section details a way to describe the provenance of a dataset, providing `GeneratedBy` with an array of objects representing pipelines or processes that generated the dataset.
+
+!!! note
+    This description can be equivalently represented using the previous section. This modeling is kept for backward-compatibility but might be removed in future BIDS releases (see BIDS 2.0).
+
+Each object in the `GeneratedBy` array includes the following REQUIRED, RECOMMENDED
+and OPTIONAL keys:
+
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_metadata_table(
+   {
+      "Name__GeneratedBy": "REQUIRED",
+      "Version__GeneratedBy": "RECOMMENDED",
+      "Description__GeneratedBy": 'RECOMMENDED if `Name` is `"Manual"`, OPTIONAL otherwise',
+      "CodeURL": "OPTIONAL",
+      "Container": "OPTIONAL"
+   }
+) }}
+
+!!! example "Example of `GeneratedBy` contents in a `dataset_description.json`"
+    ```JSON
+    {
+        "GeneratedBy": [
+            {
+              "Name": "reproin",
+              "Version": "0.6.0",
+              "Container": {
+                "Type": "docker",
+                "Tag": "repronim/reproin:0.6.0"
+              }
+            }
+        ]
+    }
+    ```
+
+## Consistency and uniqueness of identifiers
+
+The following rules and conventions are provided in order to have consistent, human readable, and explicit [IRIs](https://www.w3.org/TR/json-ld11/#iris) as identifiers for provenance objects.
+
+!!! note
+    The `Id` field contains the identifier of a provenance objects.
+
+### Identifiers for entities
+
+The identifier of an entity describing a BIDS file inside a BIDS dataset MUST be a [BIDS URI](../common-principles.md#bids-uri).
+
+!!! warning
+    The use of BIDS URIs may require to define the `DatasetLinks` object in [`dataset_description.json`](dataset-description.md#dataset_descriptionjson).
+
+For other cases listed in the [Entities](#entities) section, the identifier of an entity described in a BIDS dataset `<dataset>` SHOULD have the following form, where `<label>` is a human readable name for coherently identifying the entity and `<uid>` is a unique group of chars.
+
+```text
+bids:<dataset>:prov#<label>-<uid>
+```
+
+!!! example "Examples of identifiers for entities"
+    - `bids:ds001734:sub-002/anat/sub-02_T1w.nii` - an entity describing a T1w file for subject `sub-002` in the `ds001734` dataset;
+    - `bids::sub-014/func/sub-014_task-MGT_run-01_events.tsv` - an entity describing an events file for subject `sub-014` in the current dataset;
+    - `bids:fmriprep:sub-001/func/sub-001_task-MGT_run-01_bold_space-MNI152NLin2009cAsym_preproc.nii.gz` - an entity describing a bold file for subject `sub-001` in the `fmriprep` dataset;
+    - `bids::prov#entity-acea8093` - an entity describing a file that is not available in the dataset.
+
+### Identifiers for other provenance objects
+
+The identifier of an activity, software, or environment described in a BIDS dataset `<dataset>` SHOULD have the following form, where `<label>` is a human readable name for coherently identifying the provenance objects and `<uid>` is a unique group of chars.
+
+```text
+bids:<dataset>:prov#<label>-<uid>
+```
+
+The uniqueness of this identifier MUST be used to distinguish any activity, software, or environment that are different in any of their attributes.
+
+!!! example "Examples of identifiers for activities, environments and software"
+    - `bids:ds001734:prov#conversion-xfMMbHK1` - a conversion activity described inside the `ds001734` dataset;
+    - `bids::prov#fedora-uldfv058` - a Fedora based environment described inside the current dataset.
+    - `bids:preprocessing:prov#fmriprep-r4kzzMt8` - the fMRIPrep software described inside the `preprocessing` dataset.
+
+## Minimal examples
+
+### Provenance of a BIDS raw dataset
+
+Consider the following BIDS raw dataset:
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example(
+    {
+        "sourcedata": {
+            "dicoms": {
+                "...": "",
+            },
+        },
+        "sub-001": {
+            "anat": {
+                "sub-001_T1w.nii.gz": "",
+                "sub-001_T1w.json": ""
+            },
+        },
+        "prov": {
+            "prov-dcm2niix_act.json": "",
+            "prov-dcm2niix_soft.json": ""
+        }
+    }
+) }}
+
+The `prov/prov-dcm2niix_soft.json` file describes the software package used for the DICOM conversion. As per the [Consistency and uniqueness of identifiers](#consistency-and-uniqueness-of-identifiers) section, the identifier SHOULD start with `bids:<dataset>:prov#` (here, `bids::` refers to the current dataset).
+
+```JSON
+{
+    "Software": [
+        {
+            "Id": "bids::prov#dcm2niix-70ug8pl5",
+            "Label": "dcm2niix",
+            "Version": "v1.1.3"
+        }
+    ]
+}
+```
+
+This `prov/prov-dcm2niix_act.json` file describes the conversion activity. Note that the identifier of the previously described software package is used here to describe that the software package was used to compute this activity.
+
+```JSON
+{
+    "Activities": [
+        {
+            "Id": "bids::prov#conversion-00f3a18f",
+            "Label": "Conversion",
+            "Command": "dcm2niix -o . -f sub-%i/anat/sub-%i_T1w sourcedata/dicoms",
+            "AssociatedWith": "bids::prov#dcm2niix-70ug8pl5"
+        }
+    ]
+}
+```
+
+Inside the `sub-001/anat/sub-001_T1w.json` file, the metadata field `GeneratedBy` indicates that the `sub-001/anat/sub-001_T1w.nii.gz` file was generated by the previously described activity.
+
+```JSON
+{
+    "GeneratedBy": "bids::prov#conversion-00f3a18f"
+}
+```
+
+### Provenance of a BIDS derivative dataset
+
+Consider the following BIDS derivative dataset:
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example(
+    {
+        "sourcedata": {
+            "dicoms": {
+                "...": "",
+            },
+        },
+        "sub-001": {
+            "anat": {
+                "sub-001_T1w.nii.gz": "",
+                "sub-001_T1w.json": ""
+            },
+        },
+        "prov": {
+            "prov-dcm2niix_act.json": "",
+            "prov-dcm2niix_soft.json": ""
+        }
+    }
+) }}
+
+The `prov/prov-dcm2niix_soft.json` file describes the software package used. As per [Consistency and uniqueness of identifiers](#consistency-and-uniqueness-of-identifiers) section, the identifier SHOULD start with `bids:<dataset>:prov#` (here, `bids::` refers to the current dataset).
+
+```JSON
+{
+    "Software": [
+        {
+            "Id": "bids::prov#dcm2niix-70ug8pl5",
+            "Label": "dcm2niix",
+            "Version": "v1.1.3"
+        }
+    ]
+}
+```
+
+The `prov/prov-dcm2niix_act.json` file describes the conversion activity. Note that the identifier of the previously described software package is used here to describe that the software package was used to compute this activity.
+
+```JSON
+{
+    "Activities": [
+        {
+            "Id": "bids::prov#conversion-00f3a18f",
+            "Label": "Conversion",
+            "Command": "dcm2niix -o . -f sub-%i/anat/sub-%i_T1w sourcedata/dicoms",
+            "AssociatedWith": "bids::prov#dcm2niix-70ug8pl5"
+        }
+    ]
+}
+```
+
+Inside the `sub-001/anat/sub-001_T1w.json` file, the metadata field `GeneratedBy` indicates that the `sub-001/anat/sub-001_T1w.nii.gz` file was generated by the previously described activity.
+
+```JSON
+{
+    "GeneratedBy": "bids::prov#conversion-00f3a18f"
+}
+```
+
+### Provenance of a BIDS study dataset
+
+Consider the following BIDS study dataset:
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example(
+    {
+    "study-1": {
+        "sourcedata": {
+            "raw": {
+                "sub-01": {},
+                "sub-02": {},
+                "...": ""
+            }
+        },
+        "derivatives": {
+            "fmriprep": {}
+        },
+        "prov": {
+            "prov-fmriprep_act.json": "",
+            "prov-fmriprep_ent.json": ""
+        },
+        "dataset_description.json": "",
+        "...": ""
+    }
+   }
+) }}
+
+Inside the `dataset_description.json` file of the study dataset, dataset names are defined in order to refer to two nested datasets using BIDS URIs.
+
+```JSON
+{
+    ...
+    "DatasetLinks": {
+        "raw": "sourcedata/raw",
+        "fmriprep": "derivatives/fmriprep"
+    }
+}
+```
+
+The `prov/prov-fmriprep_ent.json` file describes two entities: one per nested dataset.
+
+```JSON
+{
+    "Entities": [
+        {
+            "Id": "bids:raw",
+            "Label": "Raw data"
+        },
+        {
+            "Id": "bids:fmriprep",
+            "Label": "Preprocessed data",
+            "GeneratedBy": "bids::prov#preprocessing-00f3a18f"
+        },
+    ]
+}
+```
+
+The `prov/prov-fmriprep_act.json` file describes the activity that generated the derivative dataset using the raw dataset.
+
+```JSON
+{
+    "Activities": [
+        {
+            "Id": "bids::prov#preprocessing-00f3a18f",
+            "Label": "Preprocessing with fMRIprep",
+            "Command": "docker run  -v sourcedata/raw:/data:ro -v derivatives/fmriprep:/out poldracklab/fmriprep:1.1.4 /data /out",
+            "Used": "bids:raw"
+        }
+    ]
+}
+```
diff --git a/src/schema/objects/datatypes.yaml b/src/schema/objects/datatypes.yaml
index 333cc4d922..cb16fa1b53 100644
--- a/src/schema/objects/datatypes.yaml
+++ b/src/schema/objects/datatypes.yaml
@@ -68,6 +68,11 @@ phenotype:
     Participant level measurement data
     (for example, responses from multiple questionnaires)
     split into individual files separate from `participants.tsv`.
+prov:
+  value: prov
+  display_name: Provenance
+  description: |
+    Provenance records describing how files in the dataset were generated.
 nirs:
   value: nirs
   display_name: Near-Infrared Spectroscopy
diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index be94a5eb0a..7ecf4a4507 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -245,6 +245,13 @@ processing:
     exploited.
   type: string
   format: label
+prov:
+  name: prov
+  display_name: Provenance group
+  description: |
+    The `prov-<label>` entity allows to group related provenance files, using an arbitrary value for `<label>`.
+  type: string
+  format: label
 reconstruction:
   name: rec
   display_name: Reconstruction
diff --git a/src/schema/objects/files.yaml b/src/schema/objects/files.yaml
index 9c6bc41305..041bc791e5 100644
--- a/src/schema/objects/files.yaml
+++ b/src/schema/objects/files.yaml
@@ -102,6 +102,13 @@ code:
     (for example the one used to generate the derivatives from the raw data).
     See the [Code section](SPEC_ROOT/modality-agnostic-files/code.md)
     for more information.
+prov:
+  display_name: Provenance Records
+  file_type: directory
+  description: |
+    A directory in which to store provenance metadata.
+    See the [Provenance section](SPEC_ROOT/modality-agnostic-files/provenance.md)
+    for more information.
 derivatives:
   display_name: Derivative data
   file_type: directory
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index e6567a57f5..9f5b332b56 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -48,6 +48,79 @@ AcquisitionVoxelSize:
     type: number
     exclusiveMinimum: 0
     unit: mm
+Activities:
+  name: Activities
+  display_name: Activities
+  description: Provenance objects describing activities.
+  type: array
+  minItems: 1
+  items:
+    type: object
+    required: [Id, Label, Command]
+    properties:
+      Id:
+        name: Id
+        description: "Identifier for the activity (see the [Consistency and uniqueness of identifiers]\
+        (SPEC_ROOT/modality-agnostic-files/provenance.md#consistency-and-uniqueness-of-identifiers) section)."
+        type: string
+        format: uri
+      Label:
+        name: Label
+        description: |
+          Name for the activity. This can be the name of the tool, script,
+          or function used (for example "bet", "recon-all", "myFunction.py", "docker").
+        type: string
+        format: label
+      Command:
+        name: Command
+        description: Command (or commands) used to run the tool, including all parameters.
+        type: string
+      AssociatedWith:
+        name: AssociatedWith
+        description: |
+          Identifier(s) of the software package(s) used to compute this activity.
+
+          Related software MUST be described as specified in the
+          [Software](SPEC_ROOT/modality-agnostic-files/provenance.md#software) section.
+        anyOf:
+          - type: string
+            format: uri
+          - type: array
+            items:
+              type: string
+              format: uri
+      Used:
+        name: Used
+        description: |
+          Identifier(s) of the entity (one or more) or environment (one or more) used by this activity.
+
+          Related entities MUST be described as specified in the
+          [Entities](SPEC_ROOT/modality-agnostic-files/provenance.md#entities) section.
+
+          Related environments MUST be described as specified in the
+          [Environments](SPEC_ROOT/modality-agnostic-files/provenance.md#environments) section.
+        anyOf:
+          - type: string
+            format: uri
+          - type: array
+            items:
+              type: string
+              format: uri
+      Type:
+        name: Type
+        description: A term from a controlled vocabulary that more specifically describes the activity.
+        type: string
+        format: uri
+      StartedAtTime:
+        name: StartedAtTime
+        description: A timestamp tracking when this activity started.
+        type: string
+        format: date
+      EndedAtTime:
+        name: EndedAtTime
+        description: A timestamp tracking when this activity ended.
+        type: string
+        format: date
 Anaesthesia:
   name: Anaesthesia
   display_name: Anaesthesia
@@ -776,7 +849,7 @@ Description__GeneratedBy:
   name: Description
   display_name: Pipeline Description
   description: |
-    Plain-text description of the pipeline or process that generated the outputs.
+    Plain-text description of the pipeline or process that generated the dataset.
     RECOMMENDED if `Name` is `"Manual"`.
   type: string
 DetectorType:
@@ -823,6 +896,14 @@ DewarPosition:
     `"upright"`, `"supine"` or `"degrees"` of angle from vertical:
     for example on CTF systems, `"upright=15°, supine=90°"`.
   type: string
+Digest:
+  name: Digest
+  display_name: Digest
+  description: |
+    Object containing checksum(s) of a file.
+    It takes the form of a dictionary with the name of the checksum functions as keys and
+    checksums as values : `{"<checksum_function>": "<checksum>"}`.
+  type: object
 DigitizedHeadPoints:
   name: DigitizedHeadPoints
   display_name: Digitized Head Points
@@ -1176,6 +1257,98 @@ EncodingTechnique:
     For example, `"Cartesian"`, `"EPSI"`, `"Spiral"`,
     or `"Density-weighted concentric ring trajectory"`.
   type: string
+Entities:
+  name: Entities
+  display_name: Entities
+  description: Provenance objects describing entities.
+  type: array
+  minItems: 1
+  items:
+    type: object
+    required: [Id, Label]
+    recommended: [Digest]
+    properties:
+      Id:
+        name: Id
+        description: "Identifier for the entity (see the [Consistency and uniqueness of identifiers]\
+        (SPEC_ROOT/modality-agnostic-files/provenance.md#consistency-and-uniqueness-of-identifiers) section)."
+        type: string
+        format: uri
+      Label:
+        name: Label
+        description: A name for the entity.
+        type: string
+        format: label
+      Digest:
+        name: Digest
+        description: |
+          For files, this includes checksums.
+          It takes the form of a dictionary with the name of the checksum functions as keys
+          and checksums as values : `{"<checksum_function>": "<checksum>"}`.
+        type: object
+      AtLocation:
+        name: AtLocation
+        description: |
+          For input files, this is the relative path to the file on disk.
+        type: string
+      GeneratedBy:
+        name: GeneratedBy
+        description: |
+          Identifier(s) of the activity (one or more) responsible for the creation of the entity.
+
+          Related activities MUST be described as specified in the
+          [Activities](SPEC_ROOT/modality-agnostic-files/provenance.md#activities) section.
+        type: array
+        minItems: 1
+        items:
+          type: string
+          format: uri
+      Type:
+        name: Type
+        description: A term from a controlled vocabulary that more specifically describes the entity.
+        type: string
+        format: uri
+EntityType:
+  name: Type
+  display_name: Type
+  description: |
+    A term from a controlled vocabulary that more specifically describes an entity.
+  type: string
+  format: uri
+Environments:
+  name: Environments
+  display_name: Environments
+  description: Provenance objects describing environments.
+  type: array
+  minItems: 1
+  items:
+    type: object
+    required: [Id, Label]
+    properties:
+      Id:
+        name: Id
+        description: "Identifier for the environment (see the [Consistency and uniqueness of identifiers]\
+        (SPEC_ROOT/modality-agnostic-files/provenance.md#consistency-and-uniqueness-of-identifiers) section)."
+        type: string
+        format: uri
+      Label:
+        name: Label
+        description: A name for the environment.
+        type: string
+        format: label
+      EnvVars:
+        name: EnvVars
+        description: A dictionary defining the environment variables as key-value pairs.
+        type: object
+      OperatingSystem:
+        name: OperatingSystem
+        description: Name of the operating system.
+        type: string
+      Dependencies:
+        name: Dependencies
+        description: |
+          A dictionary defining the software used as dependencies and their versions as key-value pairs.
+        type: object
 EpochLength:
   name: EpochLength
   display_name: Epoch Length
@@ -1375,27 +1548,45 @@ Funding:
   items:
     type: string
 GeneratedBy:
+  name: GeneratedBy
+  display_name: Generated By
+  description: Used to specify provenance of the dataset.
+  anyOf:
+    - type: array
+      minItems: 1
+      items:
+        type: object
+        required: [Name]
+        recommended: [Version]
+        properties:
+          Name:
+            $ref: objects.metadata.Name__GeneratedBy
+          Version:
+            $ref: objects.metadata.Version__GeneratedBy
+          Description:
+            $ref: objects.metadata.Description__GeneratedBy
+          CodeURL:
+            $ref: objects.metadata.CodeURL
+          Container:
+            $ref: objects.metadata.Container
+    - type: array
+      minItems: 1
+      items:
+        type: string
+        format: uri
+GeneratedById:
   name: GeneratedBy
   display_name: Generated By
   description: |
-    Used to specify provenance of the dataset.
+    Identifier(s) of the activity (one or more) responsible for the creation of the file.
+
+    Related activities MUST be described as specified in the
+    [Activities](SPEC_ROOT/modality-agnostic-files/provenance.md#activities) section.
   type: array
   minItems: 1
   items:
-    type: object
-    required: [Name]
-    recommended: [Version]
-    properties:
-      Name:
-        $ref: objects.metadata.Name__GeneratedBy
-      Version:
-        $ref: objects.metadata.Version__GeneratedBy
-      Description:
-        $ref: objects.metadata.Description__GeneratedBy
-      CodeURL:
-        $ref: objects.metadata.CodeURL
-      Container:
-        $ref: objects.metadata.Container
+    type: string
+    format: uri
 GeneticLevel:
   name: GeneticLevel
   display_name: Genetic Level
@@ -2367,7 +2558,7 @@ Name__GeneratedBy:
   name: Name
   display_name: Pipeline Name
   description: |
-    Name of the pipeline or process that generated the outputs. Use `"Manual"` to
+    Name of the pipeline or process that generated the dataset. Use `"Manual"` to
     indicate the derivatives were generated by hand, or adjusted manually after an
     initial run of an automated pipeline.
   type: string
@@ -3424,6 +3615,19 @@ ShortChannelCount:
     The number of short channels. 0 indicates no short channels.
   type: integer
   minimum: 0
+SidecarGeneratedBy:
+  name: SidecarGeneratedBy
+  display_name: Sidecar Generated By
+  description: |
+    Identifier(s) of the activity (one or more) responsible for the creation of the sidecar JSON file.
+
+    Related activities MUST be described as specified in the
+    [Activities](SPEC_ROOT/modality-agnostic-files/provenance.md#activities) section.
+  type: array
+  minItems: 1
+  items:
+    type: string
+    format: uri
 SinglesRate:
   name: SinglesRate
   display_name: Singles Rate
@@ -3492,6 +3696,48 @@ SliceTiming:
     type: number
     minimum: 0
     unit: s
+Software:
+  name: Software
+  display_name: Software
+  description: Provenance objects describing software.
+  type: array
+  minItems: 1
+  items:
+    type: object
+    required: [Id, Label, Version]
+    properties:
+      Id:
+        name: Id
+        description: "Identifier for the software package (see the [Consistency and uniqueness of identifiers]\
+        (SPEC_ROOT/modality-agnostic-files/provenance.md#consistency-and-uniqueness-of-identifiers) section)."
+        type: string
+        format: uri
+      Label:
+        name: Label
+        description: Name of the software package.
+        type: string
+        format: label
+      Version:
+        name: Version
+        description: Version of the software package.
+        type: string
+      AltIdentifier:
+        name: AltIdentifier
+        description: URI of the RRID for this software package (cf. https://rrid.site/).
+        type: string
+        format: uri
+      ActedOnBehalfOf:
+        name: ActedOnBehalfOf
+        description: |
+          Identifier of another software package that was responsible for using this software package
+          in the context of the activities associated to it.
+
+          Example: if software A launches software B to perform activity C, then B ActedOnBehalfOf A.
+
+          Related software MUST be described as specified in the
+          [Software](SPEC_ROOT/modality-agnostic-files/provenance.md#software) section.
+        type: string
+        format: uri
 SoftwareFilters:
   name: SoftwareFilters
   display_name: Software Filters
@@ -4021,7 +4267,7 @@ Version__Dataset:
 Version__GeneratedBy:
   name: Version
   display_name: Pipeline Version
-  description: Version of the pipeline
+  description: Version of the pipeline or process that generated the dataset.
   type: string
 VolumeAffineMatrix:
   name: VolumeAffineMatrix
diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index 1e2825ced2..94e0cf4815 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -502,6 +502,12 @@ VFA:
     Depending on the provided metadata fields and the sequence type,
     data may be eligible for DESPOT1, DESPOT2 and their variants
     ([Deoni et al. 2005](https://doi.org/10.1002/mrm.20314)).
+act:
+  value: act
+  display_name: Activities
+  description: |
+    A JSON file containing provenance objects describing activities.
+    (See the [`Activities`](SPEC_ROOT/modality-agnostic-files/provenance.md#activities) section).
 angio:
   value: angio
   display_name: Angiogram
@@ -612,6 +618,18 @@ electrodes:
   display_name: Electrodes
   description: |
     File that gives the location of (i)EEG electrodes.
+ent:
+  value: ent
+  display_name: Entities
+  description: |
+    A JSON file containing provenance objects describing entities.
+    (See the [`Entities`](SPEC_ROOT/modality-agnostic-files/provenance.md#entities) section).
+env:
+  value: env
+  display_name: Environments
+  description: |
+    A JSON file containing provenance objects describing environments.
+    (See the [`Environments`](SPEC_ROOT/modality-agnostic-files/provenance.md#environments) section).
 epi:
   value: epi
   display_name: EPI
@@ -817,6 +835,12 @@ probseg:
     A probabilistic segmentation.
 
     This suffix may only be used in derivative datasets.
+soft:
+  value: soft
+  display_name: Software
+  description: |
+    A JSON file containing provenance objects describing software.
+    (See the [`Software`](SPEC_ROOT/modality-agnostic-files/provenance.md#software) section).
 sbref:
   value: sbref
   display_name: Single-band reference image
diff --git a/src/schema/rules/directories.yaml b/src/schema/rules/directories.yaml
index e5415e8c14..f51ec608ee 100644
--- a/src/schema/rules/directories.yaml
+++ b/src/schema/rules/directories.yaml
@@ -53,6 +53,7 @@ raw:
       - derivatives
       - logs
       - phenotype
+      - prov
       - sourcedata
       - stimuli
       - subject
@@ -76,6 +77,10 @@ raw:
     name: phenotype
     level: optional
     opaque: false
+  prov:
+    name: prov
+    level: optional
+    opaque: false
   sourcedata:
     name: sourcedata
     level: optional
@@ -111,6 +116,7 @@ derivative:
       - derivatives
       - logs
       - phenotype
+      - prov
       - sourcedata
       - stimuli
       - subject
@@ -134,6 +140,10 @@ derivative:
     name: phenotype
     level: optional
     opaque: false
+  prov:
+    name: prov
+    level: optional
+    opaque: false
   sourcedata:
     name: sourcedata
     level: optional
diff --git a/src/schema/rules/entities.yaml b/src/schema/rules/entities.yaml
index 44174d333e..e1d118b754 100644
--- a/src/schema/rules/entities.yaml
+++ b/src/schema/rules/entities.yaml
@@ -32,3 +32,4 @@
 - density
 - label
 - description
+- prov
diff --git a/src/schema/rules/files/common/core.yaml b/src/schema/rules/files/common/core.yaml
index fe8535d0ce..d83b7cd580 100644
--- a/src/schema/rules/files/common/core.yaml
+++ b/src/schema/rules/files/common/core.yaml
@@ -36,6 +36,9 @@ code:
 derivatives:
   level: optional
   path: derivatives
+prov:
+  level: optional
+  path: prov
 docs:
   level: optional
   path: docs
diff --git a/src/schema/rules/files/common/modality_agnostic.yaml b/src/schema/rules/files/common/modality_agnostic.yaml
new file mode 100644
index 0000000000..f95295c57d
--- /dev/null
+++ b/src/schema/rules/files/common/modality_agnostic.yaml
@@ -0,0 +1,17 @@
+---
+# Files and directories that can be found at any level of a dataset.
+
+# Provenance json files
+provenance:
+  level: optional
+  datatypes:
+    - prov
+  suffixes:
+    - act
+    - ent
+    - env
+    - soft
+  extensions:
+    - .json
+  entities:
+    prov: required