diff --git a/nbqa/__main__.py b/nbqa/__main__.py
index df606cfa..dbce5f0b 100644
--- a/nbqa/__main__.py
+++ b/nbqa/__main__.py
@@ -360,7 +360,7 @@ def _run_command(  # pylint: disable=too-many-locals
     if main_command == "mypy" and "MYPY_FORCE_COLOR" not in my_env:
         my_env["MYPY_FORCE_COLOR"] = "1"
 
-    if main_command == "ruff":
+    if main_command == "ruff" and not sub_commands:
         sub_commands.insert(0, "check")
 
     if shell:
diff --git a/tests/tools/test_ruff_works.py b/tests/tools/test_ruff_works.py
index 5934c0b1..5b35e321 100644
--- a/tests/tools/test_ruff_works.py
+++ b/tests/tools/test_ruff_works.py
@@ -1,6 +1,7 @@
 """Check :code:`ruff` works as intended."""
 
 import os
+from pathlib import Path
 from typing import TYPE_CHECKING
 
 import pytest
@@ -109,3 +110,20 @@ def test_ruff_isort(capsys: "CaptureFixture") -> None:
     out, err = capsys.readouterr()
     assert out == ""
     assert err == ""
+
+
+def test_ruff_format(capsys: "CaptureFixture", tmp_notebook_for_testing: Path) -> None:
+    """
+    Should ignore cell with all magics.
+
+    Parameters
+    ----------
+    capsys
+        Pytest fixture to capture stdout and stderr.
+    """
+
+    main(["ruff format", str(tmp_notebook_for_testing)])
+
+    out, err = capsys.readouterr()
+    assert out == "1 file reformatted\n"
+    assert err == ""