diff --git a/.actions/assistant.py b/.actions/assistant.py
index e54e69e4860e7..6d1e50e26f587 100644
--- a/.actions/assistant.py
+++ b/.actions/assistant.py
@@ -459,6 +459,25 @@ def generate_docker_tags(
         tags = [f"{docker_project}:{tag}" for tag in tags]
         print(",".join(tags))
 
+    @staticmethod
+    def prune_pytest_as_errors(
+        pyproject_toml: str = "pyproject.toml", errors: tuple = ("FutureWarning", "DeprecationWarning")
+    ) -> None:
+        """Prune pytest warnings as errors from the pyproject.toml file."""
+        import tomlkit
+
+        with open(pyproject_toml, encoding="utf-8") as fopen:
+            content = fopen.read()
+        pyproject = tomlkit.parse(content)
+        filterwarnings = pyproject.get("tool", {}).get("pytest", {}).get("ini_options", {}).get("filterwarnings", [])
+        if not filterwarnings:
+            return
+        filterwarnings = [wrn for wrn in filterwarnings if not any(f"error::{err}" in wrn for err in errors)]
+        pyproject["tool"]["pytest"]["ini_options"]["filterwarnings"] = filterwarnings
+
+        with open(pyproject_toml, "w", encoding="utf-8") as fopen:
+            fopen.write(tomlkit.dumps(pyproject))
+
 
 if __name__ == "__main__":
     import jsonargparse
diff --git a/.github/workflows/ci-tests-fabric.yml b/.github/workflows/ci-tests-fabric.yml
index ef1ce3aea089c..882fea6c965c6 100644
--- a/.github/workflows/ci-tests-fabric.yml
+++ b/.github/workflows/ci-tests-fabric.yml
@@ -99,11 +99,14 @@ jobs:
       - name: Set min. dependencies
         if: ${{ matrix.config.requires == 'oldest' }}
         run: |
-          cd requirements/fabric
           uv pip install -U "lightning-utilities[cli]"
-          python -m lightning_utilities.cli requirements set-oldest --req_files "['base.txt', 'strategies.txt', 'test.txt']"
+          python -m lightning_utilities.cli requirements set-oldest \
+            --req_files "['requirements/fabric/base.txt', 'requirements/fabric/strategies.txt', 'requirements/fabric/test.txt']"
           uv pip install "cython<3.0" wheel
           uv pip install "pyyaml==5.4" --no-build-isolation
+          # This script removes any line containing "error::FutureWarning" from pyproject.toml
+          uv pip install -r requirements/ci.txt
+          python .actions/assistant.py prune_pytest_as_errors
 
       - name: Adjust PyTorch versions in requirements files
         if: ${{ matrix.config.requires != 'oldest' }}
diff --git a/.github/workflows/ci-tests-pytorch.yml b/.github/workflows/ci-tests-pytorch.yml
index 17f73aba3305d..168a6783514c3 100644
--- a/.github/workflows/ci-tests-pytorch.yml
+++ b/.github/workflows/ci-tests-pytorch.yml
@@ -98,11 +98,14 @@ jobs:
       - name: Set min. dependencies
         if: ${{ matrix.config.requires == 'oldest' }}
         run: |
-          cd requirements/pytorch
           uv pip install -U "lightning-utilities[cli]"
-          python -m lightning_utilities.cli requirements set-oldest --req_files "['base.txt', 'extra.txt', 'strategies.txt', 'examples.txt', 'test.txt']"
+          python -m lightning_utilities.cli requirements set-oldest \
+            --req_files "['requirements/pytorch/base.txt', 'requirements/pytorch/extra.txt', 'requirements/pytorch/strategies.txt', 'requirements/pytorch/examples.txt', 'requirements/pytorch/test.txt']"
           uv pip install "cython<3.0" wheel
           uv pip install "pyyaml==5.4" --no-build-isolation
+          # This script removes any line containing "error::FutureWarning" from pyproject.toml
+          uv pip install -r requirements/ci.txt
+          python .actions/assistant.py prune_pytest_as_errors
 
       - name: Adjust PyTorch versions in requirements files
         if: ${{ matrix.config.requires != 'oldest' }}
diff --git a/pyproject.toml b/pyproject.toml
index bec03d8164ad4..b4d5d0b1638f5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -182,7 +182,6 @@ filterwarnings = [
     # "error::DeprecationWarning",
     "error::FutureWarning",
     "ignore::FutureWarning:onnxscript", # Temporary ignore until onnxscript is updated
-    "ignore:The pynvml package is deprecated:FutureWarning", # Ignore pynvml deprecation warning, since it is not installed by PL directly
 ]
 xfail_strict = true
 junit_duration_report = "call"
diff --git a/requirements/ci.txt b/requirements/ci.txt
index 4aeb4e48db55c..32303d25dbe8c 100644
--- a/requirements/ci.txt
+++ b/requirements/ci.txt
@@ -6,3 +6,4 @@ importlib-metadata <9.0.0
 wget
 pkginfo ==1.12.1.2
 packaging <25.1
+tomlkit