diff --git a/internal/controllers/topology/cluster/structuredmerge/filterintent.go b/internal/controllers/topology/cluster/structuredmerge/filterintent.go
index 2b743db040d2..a8d741d1e6a1 100644
--- a/internal/controllers/topology/cluster/structuredmerge/filterintent.go
+++ b/internal/controllers/topology/cluster/structuredmerge/filterintent.go
@@ -79,6 +79,7 @@ func filterIntent(ctx *filterIntentInput) bool {
 			// Ensure we are not leaving empty maps around.
 			if v, ok := fieldCtx.value.(map[string]interface{}); ok && len(v) == 0 {
 				delete(value, field)
+				gotDeletions = true
 			}
 		}
 	}
diff --git a/internal/controllers/topology/cluster/structuredmerge/filterintent_test.go b/internal/controllers/topology/cluster/structuredmerge/filterintent_test.go
index 30be02e21277..e68f5bc6335d 100644
--- a/internal/controllers/topology/cluster/structuredmerge/filterintent_test.go
+++ b/internal/controllers/topology/cluster/structuredmerge/filterintent_test.go
@@ -167,6 +167,27 @@ func Test_filterIgnoredPaths(t *testing.T) {
 				// we are filtering out spec.foo and then spec given that it is an empty map
 			},
 		},
+		{
+			name: "Cleanup empty nested maps",
+			ctx: &filterIntentInput{
+				path: contract.Path{},
+				value: map[string]interface{}{
+					"spec": map[string]interface{}{
+						"bar": map[string]interface{}{
+							"foo": "123",
+						},
+					},
+				},
+				shouldFilter: isIgnorePath(
+					[]contract.Path{
+						{"spec", "bar", "foo"},
+					},
+				),
+			},
+			wantValue: map[string]interface{}{
+				// we are filtering out spec.bar.foo and then spec given that it is an empty map
+			},
+		},
 	}
 	for _, tt := range tests {
 		t.Run(tt.name, func(t *testing.T) {