diff --git a/beet/library/base.py b/beet/library/base.py
index e31b8772..afdfc5a6 100644
--- a/beet/library/base.py
+++ b/beet/library/base.py
@@ -810,6 +810,11 @@ def __delitem__(self, key: str):
             for i, entry in enumerate(entries):
                 if entry.get("directory") == key:
                     del entries[i]
+                    if not entries:
+                        del overlays["entries"]
+                        if not overlays:
+                            del self.pack.mcmeta.data["overlays"]
+                    break
 
     def missing(self, key: str) -> PackType:
         if self.pack is None: