diff --git a/cache.h b/cache.h
index c1c953e810..1deee48f5b 100644
--- a/cache.h
+++ b/cache.h
@@ -751,7 +751,7 @@ extern void rename_index_entry_at(struct index_state *, int pos, const char *new
 /* Remove entry, return true if there are more entries to go. */
 extern int remove_index_entry_at(struct index_state *, int pos);
 
-extern void remove_marked_cache_entries(struct index_state *istate);
+extern void remove_marked_cache_entries(struct index_state *istate, int invalidate);
 extern int remove_file_from_index(struct index_state *, const char *path);
 #define ADD_CACHE_VERBOSE 1
 #define ADD_CACHE_PRETEND 2
diff --git a/read-cache.c b/read-cache.c
index bd45dc3e24..978d43f676 100644
--- a/read-cache.c
+++ b/read-cache.c
@@ -590,13 +590,19 @@ int remove_index_entry_at(struct index_state *istate, int pos)
  * CE_REMOVE is set in ce_flags.  This is much more effective than
  * calling remove_index_entry_at() for each entry to be removed.
  */
-void remove_marked_cache_entries(struct index_state *istate)
+void remove_marked_cache_entries(struct index_state *istate, int invalidate)
 {
 	struct cache_entry **ce_array = istate->cache;
 	unsigned int i, j;
 
 	for (i = j = 0; i < istate->cache_nr; i++) {
 		if (ce_array[i]->ce_flags & CE_REMOVE) {
+			if (invalidate) {
+				cache_tree_invalidate_path(istate,
+							   ce_array[i]->name);
+				untracked_cache_remove_from_index(istate,
+								  ce_array[i]->name);
+			}
 			remove_name_hash(istate, ce_array[i]);
 			save_or_free_index_entry(istate, ce_array[i]);
 		}
diff --git a/split-index.c b/split-index.c
index 5820412dc5..8aebc3661b 100644
--- a/split-index.c
+++ b/split-index.c
@@ -162,7 +162,7 @@ void merge_base_index(struct index_state *istate)
 	ewah_each_bit(si->replace_bitmap, replace_entry, istate);
 	ewah_each_bit(si->delete_bitmap, mark_entry_for_delete, istate);
 	if (si->nr_deletions)
-		remove_marked_cache_entries(istate);
+		remove_marked_cache_entries(istate, 0);
 
 	for (i = si->nr_replacements; i < si->saved_cache_nr; i++) {
 		if (!ce_namelen(si->saved_cache[i]))
diff --git a/unpack-trees.c b/unpack-trees.c
index e8d1a6ac50..8e6afa924d 100644
--- a/unpack-trees.c
+++ b/unpack-trees.c
@@ -392,7 +392,7 @@ static int check_updates(struct unpack_trees_options *o)
 				unlink_entry(ce);
 		}
 	}
-	remove_marked_cache_entries(index);
+	remove_marked_cache_entries(index, 0);
 	remove_scheduled_dirs();
 
 	if (should_update_submodules() && o->update && !o->dry_run)