diff --git a/beets/importer/tasks.py b/beets/importer/tasks.py
index 646b64e7f..1c1d0e61e 100644
--- a/beets/importer/tasks.py
+++ b/beets/importer/tasks.py
@@ -680,6 +680,8 @@ class SingletonImportTask(ImportTask):
         return [self.item]
 
     def apply_metadata(self):
+        if config["import"]["from_scratch"]:
+            self.item.clear()
         autotag.apply_item_metadata(self.item, self.match.info)
 
     def _emit_imported(self, lib):
diff --git a/docs/changelog.rst b/docs/changelog.rst
index 2ba9f5cbd..84bb0cc02 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -90,6 +90,8 @@ Bug fixes:
 - :doc:`/plugins/ftintitle`: Fixed artist name splitting to prioritize explicit
   featuring tokens (feat, ft, featuring) over generic separators (&, and),
   preventing incorrect splits when both are present.
+- :doc:`reference/cli`: Fix 'from_scratch' option for singleton imports: delete
+  all (old) metadata when new metadata is applied. :bug:`3706`
 
 For plugin developers:
 
diff --git a/test/test_importer.py b/test/test_importer.py
index c1768df3e..6ae7d562b 100644
--- a/test/test_importer.py
+++ b/test/test_importer.py
@@ -258,6 +258,17 @@ class ImportSingletonTest(AutotagImportTestCase):
         assert self.lib.items().get().title == "Applied Track 1"
         assert (self.lib_path / "singletons" / "Applied Track 1.mp3").exists()
 
+    def test_apply_from_scratch_removes_other_metadata(self):
+        config["import"]["from_scratch"] = True
+
+        for mediafile in self.import_media:
+            mediafile.comments = "Tag Comment"
+            mediafile.save()
+
+        self.importer.add_choice(importer.Action.APPLY)
+        self.importer.run()
+        assert self.lib.items().get().comments == ""
+
     def test_skip_does_not_add_track(self):
         self.importer.add_choice(importer.Action.SKIP)
         self.importer.run()