diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1482554cf2a..e12fd17fd07 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -61,6 +61,7 @@ To learn more about active deprecations, we recommend checking [GitHub Discussio
 - TODO ([#XXX](https://github.com/kedacore/keda/issues/XXX))
 - **General**: Add --ca-dir flag to KEDA operator to specify directories with CA certificates for scalers to authenticate TLS connections (defaults to /custom/ca) ([#5860](https://github.com/kedacore/keda/issues/5860))
 - **General**: Declarative parsing of scaler config ([#5037](https://github.com/kedacore/keda/issues/5037)|[#5797](https://github.com/kedacore/keda/issues/5797))
+- **General**: Remove deprecated Kustomize commonLabels ([#5888](https://github.com/kedacore/keda/pull/5888))
 - **General**: Support for Kubernetes v1.30 ([#5828](https://github.com/kedacore/keda/issues/5828))
 
 #### Experimental
diff --git a/config/default/kustomization.yaml b/config/default/kustomization.yaml
index 71eeec6800f..4107cfec588 100644
--- a/config/default/kustomization.yaml
+++ b/config/default/kustomization.yaml
@@ -9,8 +9,10 @@
 #namePrefix: keda-
 
 # Labels to add to all resources and selectors.
-#commonLabels:
-#  someName: someValue
+# labels:
+#   - pairs:
+#       someName: someValue
+#     includeSelectors: true
 
 # [PROMETHEUS] To enable prometheus monitor, uncomment all sections with 'PROMETHEUS'.
 #- ../prometheus
diff --git a/config/minimal/kustomization.yaml b/config/minimal/kustomization.yaml
index a9a8390e9ea..e185ae4d711 100644
--- a/config/minimal/kustomization.yaml
+++ b/config/minimal/kustomization.yaml
@@ -9,8 +9,10 @@
 #namePrefix: keda-
 
 # Labels to add to all resources and selectors.
-#commonLabels:
-#  someName: someValue
+# labels:
+#   - pairs:
+#       someName: someValue
+#     includeSelectors: true
 
 # [PROMETHEUS] To enable prometheus monitor, uncomment all sections with 'PROMETHEUS'.
 #- ../prometheus
diff --git a/config/rbac/kustomization.yaml b/config/rbac/kustomization.yaml
index 27553551136..28054e74441 100644
--- a/config/rbac/kustomization.yaml
+++ b/config/rbac/kustomization.yaml
@@ -1,8 +1,11 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
-commonLabels:
-  app.kubernetes.io/name: keda-operator
-  app.kubernetes.io/part-of: keda-operator
+
+labels:
+  - pairs:
+      app.kubernetes.io/name: keda-operator
+      app.kubernetes.io/part-of: keda-operator
+    includeSelectors: true
 
 resources:
 - role.yaml