diff --git a/docs/advanced-options.md b/docs/advanced-options.md
index c4514a85..cd7b7bf4 100644
--- a/docs/advanced-options.md
+++ b/docs/advanced-options.md
@@ -33,6 +33,33 @@ Finally, note that you can _hide_ the notebook metadata in an HTML comment in `.
 
 In the `percent` and `light` script formats, magic commands (Jupyter commands prefixed by `%` or `%%`) are commented out in scripts. You can change this by using the `comment_magics` option, either in the `jupytext.toml` file or at the command line with `jupytext --opt`.
 
+## Custom language magics
+
+In Markdown and R Markdown notebooks, code blocks in languages with built-in Jupyter magic support (e.g. `javascript`, `bash`, `sql`) are automatically converted to code cells using the corresponding `%%language` magic. However, code blocks in languages not covered by built-in magics (e.g. `jsx`) remain as Markdown cells by default.
+
+If you have written custom Jupyter magics for additional languages, you can tell Jupytext about them using the `custom_language_magics` option. For example, if you have a custom `%%jsx` magic, add the following to your [`jupytext.toml`](config.md) file:
+
+```toml
+custom_language_magics = ["jsx"]
+```
+
+With this option set, Markdown code blocks like:
+
+````markdown
+```jsx
+const Hello = () => (<b>Hello</b>);
+```
+````
+
+will be converted to code cells with the `%%jsx` magic:
+
+```
+%%jsx
+const Hello = () => (<b>Hello</b>);
+```
+
+When converting a notebook (`.ipynb`) to Markdown, Jupytext automatically detects cells using non-standard language magics and records them in the `custom_language_magics` notebook metadata, ensuring that the round-trip conversion (`.ipynb` → `.md` → `.ipynb`) preserves such cells correctly.
+
 ## Active and inactive cells
 
 You might want to make some cell active only when the notebook is run in Jupyter, or active only when the `.py` file is interpreted by Python. To do so, add an `active-ipynb` tag to the cells that should only be executed in the `.ipynb` file, and an `active-py` tag to the cells that should be executed only in the Python script.
diff --git a/src/jupytext/cell_reader.py b/src/jupytext/cell_reader.py
index dc60af21..26226572 100644
--- a/src/jupytext/cell_reader.py
+++ b/src/jupytext/cell_reader.py
@@ -320,10 +320,20 @@ def __init__(self, fmt=None, default_language=None):
         self.split_at_heading = (fmt or {}).get("split_at_heading", False)
         self.in_region = False
         self.in_raw = False
+        custom_language_magics = (fmt or {}).get("custom_language_magics", [])
+        if isinstance(custom_language_magics, str):
+            custom_language_magics = [m for m in custom_language_magics.split(",") if m]
+        # Store the set of custom language magics (including upper-case variants) for matching
+        self.custom_language_magics = set(custom_language_magics) | {lang.upper() for lang in custom_language_magics}
         if self.format_version in ["1.0", "1.1"] and self.ext != ".Rmd":
             # Restore the pattern used in Markdown <= 1.1
             self.start_code_re = re.compile(r"^```(.*)")
             self.non_jupyter_code_re = re.compile(r"^```\{")
+        elif self.custom_language_magics:
+            all_languages = _JUPYTER_LANGUAGES_LOWER_AND_UPPER | self.custom_language_magics
+            self.start_code_re = re.compile(
+                r"^```(`*)(\s*)({})($|\s.*$)".format("|".join(all_languages).replace("+", "\\+"))
+            )
 
     def metadata_and_language_from_option_line(self, line):
         match_region = self.start_region_re.match(line)
@@ -352,7 +362,13 @@ def metadata_and_language_from_option_line(self, line):
 
     def options_to_metadata(self, options):
         if isinstance(options, tuple):
-            self.end_code_re = re.compile("```" + options[0])
+            # The start_code_re groups are: (extra_backticks, space, language, rest)
+            extra_backticks, _space, language, rest = options
+            self.end_code_re = re.compile("```" + extra_backticks)
+            if language in self.custom_language_magics:
+                self.cell_metadata_json = self.cell_metadata_json or is_json_metadata(rest)
+                _title, meta = text_to_metadata(rest)
+                return language, meta
             options = " ".join(options[1:])
         else:
             self.end_code_re = re.compile(r"^```\s*$")
@@ -398,7 +414,10 @@ def find_cell_end(self, lines):
                     language, metadata = self.options_to_metadata(self.start_code_re.findall(line)[0])
                     # Cells with a .noeval attribute are markdown cells #347
                     # R Markdown notebooks can have bibliography and index blocks, cf #1161 and #1429
-                    if language not in _JUPYTER_LANGUAGES_LOWER_AND_UPPER or metadata.get(".noeval", "") is None:
+                    if (
+                        language not in _JUPYTER_LANGUAGES_LOWER_AND_UPPER
+                        and language not in self.custom_language_magics
+                    ) or metadata.get(".noeval", "") is None:
                         in_explicit_code_block = True
                         prev_blank = 0
                         continue
diff --git a/src/jupytext/cell_to_text.py b/src/jupytext/cell_to_text.py
index 5972850f..b16069d5 100644
--- a/src/jupytext/cell_to_text.py
+++ b/src/jupytext/cell_to_text.py
@@ -65,7 +65,10 @@ def __init__(self, cell, default_language, fmt=None, unsupported_keys=None):
         )
         if self.parse_cell_language:
             custom_cell_magics = self.fmt.get("custom_cell_magics", "").split(",")
-            self.language, magic_args = cell_language(self.source, default_language, custom_cell_magics)
+            custom_language_magics = self.fmt.get("custom_language_magics", [])
+            if isinstance(custom_language_magics, str):
+                custom_language_magics = [m for m in custom_language_magics.split(",") if m]
+            self.language, magic_args = cell_language(self.source, default_language, custom_cell_magics + list(custom_language_magics))
 
             if magic_args:
                 self.metadata["magic_args"] = magic_args
diff --git a/src/jupytext/config.py b/src/jupytext/config.py
index 331040ca..29864bde 100644
--- a/src/jupytext/config.py
+++ b/src/jupytext/config.py
@@ -173,6 +173,15 @@ class JupytextConfiguration(Configurable):
         config=True,
     )
 
+    custom_language_magics = List(
+        Unicode(),
+        help="A list of additional language magics. Use e.g. "
+        'custom_language_magics = ["jsx", "tsx"] if you have custom magics for those languages '
+        "and want Markdown code blocks in those languages to be converted to code cells "
+        "with the appropriate cell magic.",
+        config=True,
+    )
+
     def set_default_format_options(self, format_options, read=False):
         """Set default format option"""
         if self.default_notebook_metadata_filter:
@@ -216,6 +225,8 @@ def set_default_format_options(self, format_options, read=False):
             format_options.setdefault("rst2md", self.sphinx_convert_rst2md)
         if self.custom_cell_magics:
             format_options.setdefault("custom_cell_magics", self.custom_cell_magics)
+        if self.custom_language_magics:
+            format_options.setdefault("custom_language_magics", self.custom_language_magics)
 
     def default_formats(self, path):
         """Return the default formats, if they apply to the current path #157"""
diff --git a/src/jupytext/formats.py b/src/jupytext/formats.py
index a5234248..3a164eaf 100644
--- a/src/jupytext/formats.py
+++ b/src/jupytext/formats.py
@@ -706,6 +706,7 @@ def short_form_multiple_formats(jupytext_formats: list[dict[str, str]]) -> str:
     "cell_metadata_filter",
     "cell_markers",
     "custom_cell_magics",
+    "custom_language_magics",
 ]
 _VALID_FORMAT_NAMES = {fmt.format_name for fmt in JUPYTEXT_FORMATS}
 
diff --git a/src/jupytext/jupytext.py b/src/jupytext/jupytext.py
index f714d5e8..21657abe 100644
--- a/src/jupytext/jupytext.py
+++ b/src/jupytext/jupytext.py
@@ -34,6 +34,7 @@
     metadata_to_metadata_and_cell,
 )
 from .languages import (
+    _JUPYTER_LANGUAGES_LOWER_AND_UPPER,
     _SCRIPT_EXTENSIONS,
     default_language_from_metadata_and_ext,
     set_main_and_cell_language,
@@ -146,7 +147,10 @@ def reads(self, s, **_):
             lines = lines[pos:]
 
         custom_cell_magics = self.fmt.get("custom_cell_magics", "").split(",")
-        set_main_and_cell_language(metadata, cells, self.implementation.extension, custom_cell_magics)
+        custom_language_magics = self.fmt.get("custom_language_magics", [])
+        if isinstance(custom_language_magics, str):
+            custom_language_magics = [m for m in custom_language_magics.split(",") if m]
+        set_main_and_cell_language(metadata, cells, self.implementation.extension, custom_cell_magics + list(custom_language_magics))
         cell_metadata = set()
         for cell in cells:
             cell_metadata.update(cell.metadata.keys())
@@ -242,6 +246,24 @@ def writes(self, nb, metadata=None, **kwargs):
                     self.fmt["use_runtools"] = True
                     break
 
+        # Auto-detect non-standard language magics and record them in custom_language_magics
+        if self.ext in [".md", ".markdown", ".Rmd"]:
+            custom_cell_magics_list = self.fmt.get("custom_cell_magics", "").split(",")
+            existing_custom_language_magics = self.fmt.get("custom_language_magics", [])
+            if isinstance(existing_custom_language_magics, str):
+                existing_custom_language_magics = [m for m in existing_custom_language_magics.split(",") if m]
+            detected_magics = set(existing_custom_language_magics)
+            for cell in nb.cells:
+                if cell.cell_type == "code" and cell.source:
+                    first_line = cell.source.split("\n")[0]
+                    if first_line.startswith("%%"):
+                        lang = first_line[2:].split(" ")[0].strip()
+                        if lang and lang not in _JUPYTER_LANGUAGES_LOWER_AND_UPPER and lang not in custom_cell_magics_list:
+                            detected_magics.add(lang)
+            if detected_magics != set(existing_custom_language_magics):
+                self.fmt["custom_language_magics"] = sorted(detected_magics)
+                metadata.setdefault("jupytext", {})["custom_language_magics"] = self.fmt["custom_language_magics"]
+
         header = encoding_and_executable(nb, metadata, self.ext)
         unsupported_keys = set()
         header_content, header_lines_to_next_cell = metadata_and_cell_to_header(
diff --git a/tests/functional/others/test_custom_language_magics.py b/tests/functional/others/test_custom_language_magics.py
new file mode 100644
index 00000000..6c4e0644
--- /dev/null
+++ b/tests/functional/others/test_custom_language_magics.py
@@ -0,0 +1,111 @@
+import nbformat
+import pytest
+from nbformat.v4.nbbase import new_code_cell, new_markdown_cell, new_notebook
+
+import jupytext
+from jupytext.cli import jupytext as jupytext_cli
+from jupytext.compare import compare_notebooks
+from jupytext.languages import _JUPYTER_LANGUAGES_LOWER_AND_UPPER
+
+
+def test_custom_language_magics_md_to_ipynb(tmpdir):
+    """Code blocks in custom language magics should be converted to code cells"""
+    assert "jsx" not in _JUPYTER_LANGUAGES_LOWER_AND_UPPER
+
+    # Pass custom_language_magics directly via fmt options
+    md = """```python
+print("hello")
+```
+
+```jsx
+const Hello = () => (Hello);
+```
+"""
+    nb = jupytext.reads(md, fmt={"extension": ".md", "custom_language_magics": ["jsx"]})
+    assert len(nb.cells) == 2
+    assert nb.cells[0].cell_type == "code"
+    assert nb.cells[0].source == 'print("hello")'
+    assert nb.cells[1].cell_type == "code"
+    assert nb.cells[1].source == "%%jsx\nconst Hello = () => (Hello);"
+
+
+def test_custom_language_magics_ipynb_to_md(tmpdir):
+    """When writing to markdown with non-standard magic, custom_language_magics is auto-detected"""
+    assert "jsx" not in _JUPYTER_LANGUAGES_LOWER_AND_UPPER
+
+    nb = new_notebook(
+        cells=[
+            new_code_cell('print("hello")'),
+            new_code_cell("%%jsx\nconst Hello = () => (<b>Hello</b>);"),
+        ]
+    )
+
+    md = jupytext.writes(nb, fmt="md")
+    assert "custom_language_magics:" in md
+    assert "jsx" in md
+    assert "```jsx" in md
+
+
+def test_custom_language_magics_roundtrip(tmpdir):
+    """Round-trip: md with custom language magic -> ipynb -> md should preserve the code cell"""
+    assert "jsx" not in _JUPYTER_LANGUAGES_LOWER_AND_UPPER
+
+    nb = new_notebook(
+        cells=[
+            new_code_cell('print("hello")'),
+            new_code_cell("%%jsx\nconst Hello = () => (<b>Hello</b>);"),
+        ]
+    )
+
+    # ipynb -> md
+    md = jupytext.writes(nb, fmt="md")
+    assert "```jsx" in md
+
+    # md -> ipynb
+    nb2 = jupytext.reads(md, fmt="md")
+    assert len(nb2.cells) == 2
+    assert nb2.cells[1].cell_type == "code"
+    assert nb2.cells[1].source == "%%jsx\nconst Hello = () => (<b>Hello</b>);"
+
+
+def test_custom_language_magics_config_file(tmpdir):
+    """custom_language_magics from jupytext.toml should allow md -> ipynb conversion"""
+    assert "jsx" not in _JUPYTER_LANGUAGES_LOWER_AND_UPPER
+
+    cfg_file = tmpdir.join("jupytext.toml")
+    cfg_file.write('custom_language_magics = ["jsx"]')
+
+    md_file = tmpdir.join("notebook.md")
+    nb_file = tmpdir.join("notebook.ipynb")
+
+    md_file.write(
+        """```python
+print("hello")
+```
+
+```jsx
+const Hello = () => (<b>Hello</b>);
+```
+"""
+    )
+
+    jupytext_cli([str(md_file), "--to", "notebook"])
+    nb = nbformat.read(str(nb_file), as_version=4)
+
+    assert len(nb.cells) == 2
+    assert nb.cells[1].cell_type == "code"
+    assert nb.cells[1].source == "%%jsx\nconst Hello = () => (<b>Hello</b>);"
+
+
+def test_custom_language_magics_not_markdown_cell(tmpdir):
+    """Without custom_language_magics, jsx code blocks should remain as markdown cells"""
+    assert "jsx" not in _JUPYTER_LANGUAGES_LOWER_AND_UPPER
+
+    md = """```jsx
+const Hello = () => (<b>Hello</b>);
+```
+"""
+    nb = jupytext.reads(md, fmt="md")
+    # Without custom_language_magics, this should be a markdown cell
+    assert len(nb.cells) == 1
+    assert nb.cells[0].cell_type == "markdown"