diff --git a/CHANGELOG.md b/CHANGELOG.md
index 560c53118de..c44c39d1dfb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -28,6 +28,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 - The [HtmlToLaTeXFormatter](https://docs.jabref.org/finding-sorting-and-cleaning-entries/saveactions#html-to-latex) keeps single `<` characters.
 - We fixed a performance regression when opening large libraries [#9041](https://github.com/JabRef/jabref/issues/9041)
+- Saving after adding a subgroup and removing it do not cause a change notification anymore. [#9064](https://github.com/JabRef/jabref/issues/9064)
 - We fixed a bug where spaces are trimmed when highlighting differences in the Entries merge dialog. [koppor#371](https://github.com/koppor/jabref/issues/371)
 
 ### Removed
diff --git a/src/main/java/org/jabref/logic/bibtex/comparator/GroupDiff.java b/src/main/java/org/jabref/logic/bibtex/comparator/GroupDiff.java
index 35c2e5a1338..0877e6e37af 100644
--- a/src/main/java/org/jabref/logic/bibtex/comparator/GroupDiff.java
+++ b/src/main/java/org/jabref/logic/bibtex/comparator/GroupDiff.java
@@ -22,13 +22,20 @@ public static Optional<GroupDiff> compare(MetaData originalMetaData, MetaData ne
         final Optional<GroupTreeNode> originalGroups = originalMetaData.getGroups();
         final Optional<GroupTreeNode> newGroups = newMetaData.getGroups();
 
-        if (!originalGroups.equals(newGroups)) {
+        // special case: the data model may contain the single "All Entries" group without any children
+        boolean bothGroupsAreEmpty = groupsAreEmpty(originalGroups) && groupsAreEmpty(newGroups);
+
+        if (!originalGroups.equals(newGroups) && !bothGroupsAreEmpty) {
             return Optional.of(new GroupDiff(originalGroups.orElse(null), newGroups.orElse(null)));
         } else {
             return Optional.empty();
         }
     }
 
+    private static boolean groupsAreEmpty(Optional<GroupTreeNode> groups) {
+        return groups.map(g -> g.getChildren().isEmpty()).orElse(true);
+    }
+
     public GroupTreeNode getOriginalGroupRoot() {
         return originalGroupRoot;
     }