diff --git a/libcst/codemod/_cli.py b/libcst/codemod/_cli.py
index 4726a34f5..8a57b491e 100644
--- a/libcst/codemod/_cli.py
+++ b/libcst/codemod/_cli.py
@@ -245,10 +245,13 @@ def _execute_transform(  # noqa: C901
         # We do this after the fork so that a context that was initialized with
         # some defaults before calling parallel_exec_transform_with_prettyprint
         # will be updated per-file.
+        # We should clean the warnings array as well, otherwise warnings will be
+        # passed from previous file
         transformer.context = replace(
             transformer.context,
             filename=filename,
             scratch={},
+            warnings=[],
         )
 
         # attempt to work out the module and package name for this file
diff --git a/libcst/codemod/tests/test_codemod_cli.py b/libcst/codemod/tests/test_codemod_cli.py
index 934ae6678..a22e17570 100644
--- a/libcst/codemod/tests/test_codemod_cli.py
+++ b/libcst/codemod/tests/test_codemod_cli.py
@@ -7,11 +7,12 @@
 
 import subprocess
 import sys
+import tempfile
 from pathlib import Path
 
 from libcst._parser.entrypoints import is_native
 from libcst.testing.utils import UnitTest
-
+from libcst.codemod import CodemodTest
 
 class TestCodemodCLI(UnitTest):
     def test_codemod_formatter_error_input(self) -> None:
@@ -38,3 +39,34 @@ def test_codemod_formatter_error_input(self) -> None:
                 "error: cannot format -: Cannot parse: 13:10:     async with AsyncExitStack() as stack:",
                 rlt.stderr.decode("utf-8"),
             )
+
+    def test_warning_messages_several_files(self) -> None:
+        mod = """
+        def baz() -> str:
+            return "{}: {}".format(*baz)
+
+        def foobar() -> str:
+            return "{x}: {y}".format(**baz)
+        """
+        with tempfile.TemporaryDirectory() as root:
+            p = Path(root)
+            (p / "mod1.py").write_text(CodemodTest.make_fixture_data(mod))
+            (p / "mod2.py").write_text(CodemodTest.make_fixture_data(mod))
+            (p / "mod3.py").write_text(CodemodTest.make_fixture_data(mod))
+            rlt = subprocess.run(
+                [
+                    "python",
+                    "-m",
+                    "libcst.tool",
+                    "codemod",
+                    "convert_format_to_fstring.ConvertFormatStringCommand",
+                    p,
+                ],
+                stdout=subprocess.PIPE,
+                stderr=subprocess.PIPE,
+            )
+            # Each module will generate 2 warnings, so we should get 6 warnings in total
+            self.assertIn(
+                "- 6 warnings were generated.",
+                rlt.stderr.decode("utf-8"),
+            )