diff --git a/beets/util/extension.py b/beets/util/extension.py
index 7b87a98c93..fb3d7da493 100644
--- a/beets/util/extension.py
+++ b/beets/util/extension.py
@@ -170,7 +170,12 @@ def remux_mpeglayer3_wav(path: AnyPath) -> AnyPath | None:
     mp3_path = syspath.with_suffix(".mp3")
     mp3_path.write_bytes(mp3_data)
 
-    util.remove(path)
+    # When the source already has an `.mp3` extension, it has just been
+    # rewritten in place with the extracted stream, so there is no separate
+    # original left to remove. Compare with `samefile` so that a case-only
+    # difference on a case-insensitive filesystem is caught too.
+    if not util.samefile(mp3_path, syspath):
+        util.remove(path)
 
     if isinstance(path, str):
         return str(mp3_path)
diff --git a/docs/changelog.rst b/docs/changelog.rst
index acbd3294fe..b5b318366e 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -95,6 +95,10 @@ Bug fixes
   valid date/time string" error instead of crashing with an uncaught
   ``KeyError``. A ``|`` was being accepted as a relative-date unit due to a
   regular expression character-class typo.
+- ``remux_mp3_in_wav`` no longer deletes the imported file when a
+  MPEGLAYER3 WAV has an ``.mp3`` extension: the remuxed stream was written back
+  to the same path and then removed as if it were a leftover original.
+  :bug:`6748`
 
 ..
     For plugin developers
diff --git a/test/test_importer.py b/test/test_importer.py
index c626202c7b..44a2a32bfc 100644
--- a/test/test_importer.py
+++ b/test/test_importer.py
@@ -1894,6 +1894,32 @@ def test_remux_mpeglayer3_wav(self):
         assert mp3_path.exists()
         assert not dest.exists()
 
+    def test_remux_mpeglayer3_wav_mp3_extension(self):
+        """A MPEGLAYER3 WAV with an `.mp3` extension must not be deleted.
+
+        See #6748.
+        """
+        src = _common.RSRC / "mpeglayer3.wav"
+        dest = self.temp_path / "mpeglayer3.mp3"
+        shutil.copy(syspath(src), syspath(dest))
+
+        mp3_path = remux_mpeglayer3_wav(dest)
+
+        assert mp3_path == dest
+        assert dest.exists()
+
+    def test_remux_mpeglayer3_wav_mp3_extension_uppercase(self):
+        """The same holds when the extension differs only by case."""
+        src = _common.RSRC / "mpeglayer3.wav"
+        dest = self.temp_path / "mpeglayer3.MP3"
+        shutil.copy(syspath(src), syspath(dest))
+
+        mp3_path = remux_mpeglayer3_wav(dest)
+
+        assert dest.exists()
+        assert mp3_path is not None
+        assert mp3_path.exists()
+
     def test_remux_mpeglayer3_wav_disabled(self):
         """When remux_mp3_in_wav is disabled, WAV file should not be remuxed."""
         self.config["import"]["remux_mp3_in_wav"] = False