diff --git a/CHANGES.md b/CHANGES.md
index 405b71a6c2f..11e491e1c65 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -21,6 +21,7 @@
 
 - Fix crashes involving comments in parenthesised return types or `X | Y` style unions.
   (#4453)
+- Fix skipping Jupyter cells with unknown `%%` magic (#4462)
 
 ### Preview style
 
diff --git a/src/black/__init__.py b/src/black/__init__.py
index 2640e17c003..a94f7fc29a0 100644
--- a/src/black/__init__.py
+++ b/src/black/__init__.py
@@ -53,12 +53,12 @@
 )
 from black.handle_ipynb_magics import (
     PYTHON_CELL_MAGICS,
-    TRANSFORMED_MAGICS,
     jupyter_dependencies_are_installed,
     mask_cell,
     put_trailing_semicolon_back,
     remove_trailing_semicolon,
     unmask_cell,
+    validate_cell,
 )
 from black.linegen import LN, LineGenerator, transform_line
 from black.lines import EmptyLineTracker, LinesBlock
@@ -1084,32 +1084,6 @@ def format_file_contents(
     return dst_contents
 
 
-def validate_cell(src: str, mode: Mode) -> None:
-    """Check that cell does not already contain TransformerManager transformations,
-    or non-Python cell magics, which might cause tokenizer_rt to break because of
-    indentations.
-
-    If a cell contains ``!ls``, then it'll be transformed to
-    ``get_ipython().system('ls')``. However, if the cell originally contained
-    ``get_ipython().system('ls')``, then it would get transformed in the same way:
-
-        >>> TransformerManager().transform_cell("get_ipython().system('ls')")
-        "get_ipython().system('ls')\n"
-        >>> TransformerManager().transform_cell("!ls")
-        "get_ipython().system('ls')\n"
-
-    Due to the impossibility of safely roundtripping in such situations, cells
-    containing transformed magics will be ignored.
-    """
-    if any(transformed_magic in src for transformed_magic in TRANSFORMED_MAGICS):
-        raise NothingChanged
-    if (
-        src[:2] == "%%"
-        and src.split()[0][2:] not in PYTHON_CELL_MAGICS | mode.python_cell_magics
-    ):
-        raise NothingChanged
-
-
 def format_cell(src: str, *, fast: bool, mode: Mode) -> str:
     """Format code in given cell of Jupyter notebook.
 
diff --git a/src/black/handle_ipynb_magics.py b/src/black/handle_ipynb_magics.py
index 4fe88f1f76f..792d22595aa 100644
--- a/src/black/handle_ipynb_magics.py
+++ b/src/black/handle_ipynb_magics.py
@@ -3,6 +3,7 @@
 import ast
 import collections
 import dataclasses
+import re
 import secrets
 import sys
 from functools import lru_cache
@@ -14,6 +15,7 @@
 else:
     from typing_extensions import TypeGuard
 
+from black.mode import Mode
 from black.output import out
 from black.report import NothingChanged
 
@@ -64,6 +66,34 @@ def jupyter_dependencies_are_installed(*, warn: bool) -> bool:
     return installed
 
 
+def validate_cell(src: str, mode: Mode) -> None:
+    """Check that cell does not already contain TransformerManager transformations,
+    or non-Python cell magics, which might cause tokenizer_rt to break because of
+    indentations.
+
+    If a cell contains ``!ls``, then it'll be transformed to
+    ``get_ipython().system('ls')``. However, if the cell originally contained
+    ``get_ipython().system('ls')``, then it would get transformed in the same way:
+
+        >>> TransformerManager().transform_cell("get_ipython().system('ls')")
+        "get_ipython().system('ls')\n"
+        >>> TransformerManager().transform_cell("!ls")
+        "get_ipython().system('ls')\n"
+
+    Due to the impossibility of safely roundtripping in such situations, cells
+    containing transformed magics will be ignored.
+    """
+    if any(transformed_magic in src for transformed_magic in TRANSFORMED_MAGICS):
+        raise NothingChanged
+
+    line = _get_code_start(src)
+    if line.startswith("%%") and (
+        line.split(maxsplit=1)[0][2:]
+        not in PYTHON_CELL_MAGICS | mode.python_cell_magics
+    ):
+        raise NothingChanged
+
+
 def remove_trailing_semicolon(src: str) -> tuple[str, bool]:
     """Remove trailing semicolon from Jupyter notebook cell.
 
@@ -276,6 +306,21 @@ def unmask_cell(src: str, replacements: list[Replacement]) -> str:
     return src
 
 
+def _get_code_start(src: str) -> str:
+    """Provides the first line where the code starts.
+
+    Iterates over lines of code until it finds the first line that doesn't
+    contain only empty spaces and comments. It removes any empty spaces at the
+    start of the line and returns it. If such line doesn't exist, it returns an
+    empty string.
+    """
+    for match in re.finditer(".+", src):
+        line = match.group(0).lstrip()
+        if line and not line.startswith("#"):
+            return line
+    return ""
+
+
 def _is_ipython_magic(node: ast.expr) -> TypeGuard[ast.Attribute]:
     """Check if attribute is IPython magic.
 
diff --git a/tests/test_ipynb.py b/tests/test_ipynb.py
index 59897190304..bdc2f27fcdb 100644
--- a/tests/test_ipynb.py
+++ b/tests/test_ipynb.py
@@ -208,6 +208,22 @@ def test_cell_magic_with_custom_python_magic(
         assert result == expected_output
 
 
+@pytest.mark.parametrize(
+    "src",
+    (
+        "   %%custom_magic \nx=2",
+        "\n\n%%custom_magic\nx=2",
+        "# comment\n%%custom_magic\nx=2",
+        "\n  \n # comment with %%time\n\t\n %%custom_magic # comment \nx=2",
+    ),
+)
+def test_cell_magic_with_custom_python_magic_after_spaces_and_comments_noop(
+    src: str,
+) -> None:
+    with pytest.raises(NothingChanged):
+        format_cell(src, fast=True, mode=JUPYTER_MODE)
+
+
 def test_cell_magic_nested() -> None:
     src = "%%time\n%%time\n2+2"
     result = format_cell(src, fast=True, mode=JUPYTER_MODE)