diff --git a/beets/importer/tasks.py b/beets/importer/tasks.py
index 75f04cf5a..4aa1f8a62 100644
--- a/beets/importer/tasks.py
+++ b/beets/importer/tasks.py
@@ -690,6 +690,8 @@ 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 88b82e4da..bf830bade 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -39,6 +39,9 @@ Bug fixes:
   :bug:`5797`
 * :doc:`plugins/musicbrainz`: Fix the MusicBrainz search not taking into
   account the album/recording aliases
+* :doc:`reference/cli`: Fix 'from_scratch' option for singleton imports: delete
+  all (old) metadata when new metadata is applied.
+  :bug:`3706`
 
 For packagers:
 
diff --git a/test/test_importer.py b/test/test_importer.py
index 9bb0e8a63..2fa5b32d3 100644
--- a/test/test_importer.py
+++ b/test/test_importer.py
@@ -315,6 +315,17 @@ class ImportSingletonTest(AutotagImportTestCase):
         self.importer.run()
         self.assert_file_in_lib(b"singletons", b"Applied Track 1.mp3")
 
+    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_first_track(self):
         self.importer.add_choice(importer.Action.SKIP)
         self.importer.run()