diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7be31d38c84..2ca9127cd5e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,7 +24,7 @@
 
 ### Improvements
 
-- TODO ([#XXX](https://github.com/kedacore/keda/pull/XXXX))
+- Remove app.kubernetes.io/version label from label selectors ([#1696](https://github.com/kedacore/keda/pull/1696))
 
 ### Breaking Changes
 
diff --git a/Makefile b/Makefile
index b99a3cfe1eb..1c6b916f0b8 100644
--- a/Makefile
+++ b/Makefile
@@ -88,8 +88,10 @@ release: manifests kustomize set-version
 	$(KUSTOMIZE) edit set image ghcr.io/kedacore/keda=${IMAGE_CONTROLLER}
 	cd config/metrics-server && \
     $(KUSTOMIZE) edit set image ghcr.io/kedacore/keda-metrics-apiserver=${IMAGE_ADAPTER}
-	cd config/default && \
-    $(KUSTOMIZE) edit add label -f app.kubernetes.io/version:${VERSION}
+	# Need this workaround to mitigate a problem with inserting labels into selectors,
+	# until this issue is solved: https://github.com/kubernetes-sigs/kustomize/issues/1009
+	@sed -i".out" -e 's@version:[ ].*@version: $(VERSION)@g' config/default/kustomize-config/metadataLabelTransformer.yaml
+	rm -rf config/default/kustomize-config/metadataLabelTransformer.yaml.out
 	$(KUSTOMIZE) build config/default > keda-$(VERSION).yaml
 
 .PHONY: set-version
@@ -122,8 +124,10 @@ deploy: manifests kustomize
 	$(KUSTOMIZE) edit set image ghcr.io/kedacore/keda=${IMAGE_CONTROLLER}
 	cd config/metrics-server && \
     $(KUSTOMIZE) edit set image ghcr.io/kedacore/keda-metrics-apiserver=${IMAGE_ADAPTER}
-	cd config/default && \
-    $(KUSTOMIZE) edit add label -f app.kubernetes.io/version:${VERSION}
+	# Need this workaround to mitigate a problem with inserting labels into selectors,
+	# until this issue is solved: https://github.com/kubernetes-sigs/kustomize/issues/1009
+	@sed -i".out" -e 's@version:[ ].*@version: $(VERSION)@g' config/default/kustomize-config/metadataLabelTransformer.yaml
+	rm -rf config/default/kustomize-config/metadataLabelTransformer.yaml.out
 	$(KUSTOMIZE) build config/default | kubectl apply -f -
 
 # Undeploy controller
diff --git a/config/default/kustomization.yaml b/config/default/kustomization.yaml
index 687c44442ed..cdf3a30e51c 100644
--- a/config/default/kustomization.yaml
+++ b/config/default/kustomization.yaml
@@ -17,10 +17,10 @@
 
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
-commonLabels:
-  app.kubernetes.io/part-of: keda-operator
-  app.kubernetes.io/version: main
-
+# Need this transformer to mitigate a problem with inserting labels into selectors,
+# until this issue is solved: https://github.com/kubernetes-sigs/kustomize/issues/1009
+transformers:
+- kustomize-config/metadataLabelTransformer.yaml
 
 resources:
 - ../crd
diff --git a/config/default/kustomize-config/metadataLabelTransformer.yaml b/config/default/kustomize-config/metadataLabelTransformer.yaml
new file mode 100644
index 00000000000..a9deb62005b
--- /dev/null
+++ b/config/default/kustomize-config/metadataLabelTransformer.yaml
@@ -0,0 +1,10 @@
+apiVersion: builtin
+kind: LabelTransformer
+metadata:
+  name: metadataLabelTransformer
+labels:
+  app.kubernetes.io/version: main
+  app.kubernetes.io/part-of: keda-operator
+fieldSpecs:
+- path: metadata/labels
+  create: true