diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9c7ef562c..33e394eab 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ Find out more about isort's release policy [here](https://pycqa.github.io/isort/
   - Implemented #1737: Support for using action comments to avoid adding imports to individual files.
   - Implemented #1750: Ability to customize output format lines.
   - Implemented #1732: Support for custom sort functions.
+  - Implemented #1722: Improved behavior for running isort in atomic mode over Cython source files.
   - Fixed (https://github.com/PyCQA/isort/pull/1695): added imports being added to doc string in some cases.
   - Fixed (https://github.com/PyCQA/isort/pull/1714): in rare cases line continuation combined with tabs can output invalid code.
   - Fixed (https://github.com/PyCQA/isort/pull/1726): isort ignores reverse_sort when force_sort_within_sections is true.
diff --git a/isort/api.py b/isort/api.py
index fcc0bd231..31e433cfa 100644
--- a/isort/api.py
+++ b/isort/api.py
@@ -37,7 +37,7 @@
 from .io import Empty, File
 from .place import module as place_module  # noqa: F401
 from .place import module_with_reason as place_module_with_reason  # noqa: F401
-from .settings import DEFAULT_CONFIG, Config
+from .settings import CYTHON_EXTENSIONS, DEFAULT_CONFIG, Config
 
 
 class ImportKey(Enum):
@@ -193,9 +193,14 @@ def sort_stream(
         try:
             file_content = input_stream.read()
             compile(file_content, content_source, "exec", 0, 1)
-            input_stream = StringIO(file_content)
         except SyntaxError:
-            raise ExistingSyntaxErrors(content_source)
+            if extension not in CYTHON_EXTENSIONS:
+                raise ExistingSyntaxErrors(content_source)
+            elif config.verbose:
+                warn(
+                    f"{content_source} Python AST errors found but ignored due to Cython extension"
+                )
+        input_stream = StringIO(file_content)
 
         if not output_stream.readable():
             _internal_output = StringIO()
@@ -216,10 +221,15 @@ def sort_stream(
         try:
             compile(_internal_output.read(), content_source, "exec", 0, 1)
             _internal_output.seek(0)
-            if _internal_output != output_stream:
-                output_stream.write(_internal_output.read())
         except SyntaxError:  # pragma: no cover
-            raise IntroducedSyntaxErrors(content_source)
+            if extension not in CYTHON_EXTENSIONS:
+                raise IntroducedSyntaxErrors(content_source)
+            elif config.verbose:
+                warn(
+                    f"{content_source} Python AST errors found but ignored due to Cython extension"
+                )
+        if _internal_output != output_stream:
+            output_stream.write(_internal_output.read())
 
     return changed
 
diff --git a/isort/settings.py b/isort/settings.py
index 9eafb8644..b17488bf2 100644
--- a/isort/settings.py
+++ b/isort/settings.py
@@ -47,7 +47,8 @@
 from .wrap_modes import from_string as wrap_mode_from_string
 
 _SHEBANG_RE = re.compile(br"^#!.*\bpython[23w]?\b")
-SUPPORTED_EXTENSIONS = frozenset({"py", "pyi", "pyx", "pxd"})
+CYTHON_EXTENSIONS = frozenset({"pyx", "pxd"})
+SUPPORTED_EXTENSIONS = frozenset({"py", "pyi", *CYTHON_EXTENSIONS})
 BLOCKED_EXTENSIONS = frozenset({"pex"})
 FILE_SKIP_COMMENTS: Tuple[str, ...] = (
     "isort:" + "skip_file",
diff --git a/tests/unit/test_isort.py b/tests/unit/test_isort.py
index 0599925e7..c90f40d29 100644
--- a/tests/unit/test_isort.py
+++ b/tests/unit/test_isort.py
@@ -1408,6 +1408,17 @@ def test_atomic_mode() -> None:
     with pytest.raises(ExistingSyntaxErrors):
         isort.code(test_input, atomic=True)
 
+    # unless file is for Cython which doesn't yet provide a public AST parsing API
+    assert (
+        isort.code(test_input, extension="pyx", atomic=True, verbose=True)
+        == isort.code(test_input, extension="pyx", atomic=True)
+        == """from a import e, f
+from b import c, d
+
+while True print 'Hello world'
+"""
+    )
+
     # ensure atomic works with streams
     test_input = as_stream("from b import d, c\nfrom a import f, e\n")
     test_output = UnreadableStream()