diff --git a/Makefile b/Makefile
index 55df33ffa1..9d2484de91 100644
--- a/Makefile
+++ b/Makefile
@@ -111,7 +111,7 @@ build: generate fmt vet ## Build manager binary.
 	go build -o bin/manager main.go
 
 .PHONY: run
-run: manifests build ## Run a controller from your host.
+run: manifests install create-kyma-system-ns build ## Run a controller from your host.
 	ISTIO_INSTALL_BIN_PATH=$(ISTIO_INSTALL_BIN_PATH) go run ./main.go
 
 .PHONY: docker-build
@@ -138,6 +138,10 @@ ifndef ignore-not-found
   ignore-not-found = false
 endif
 
+.PHONY: create-kyma-system-ns
+create-kyma-system-ns:
+	kubectl create namespace kyma-system --dry-run=client -o yaml | kubectl apply -f -
+
 .PHONY: install
 install: manifests kustomize ## Install CRDs into the K8s cluster specified in ~/.kube/config.
 	$(KUSTOMIZE) build config/crd | kubectl apply -f -
@@ -147,7 +151,7 @@ uninstall: manifests kustomize ## Uninstall CRDs from the K8s cluster specified
 	$(KUSTOMIZE) build config/crd | kubectl delete --ignore-not-found=$(ignore-not-found) -f -
 
 .PHONY: deploy
-deploy: manifests kustomize ## Deploy controller to the K8s cluster specified in ~/.kube/config.
+deploy: create-kyma-system-ns manifests kustomize ## Deploy controller to the K8s cluster specified in ~/.kube/config.
 	cd config/manager && $(KUSTOMIZE) edit set image controller=${IMG}
 	$(KUSTOMIZE) build config/default | kubectl apply -f -
 
@@ -255,7 +259,7 @@ istio-integration-test: install deploy
 	cd tests/integration && TEST_REQUEST_TIMEOUT=300s && EXPORT_RESULT=true go test -v -timeout 35m -run TestIstioMain
 
 .PHONY: deploy-latest-release
-deploy-latest-release:
+deploy-latest-release: create-kyma-system-ns
 	cd tests/integration && ./scripts/deploy-latest-release-to-cluster.sh $(TARGET_BRANCH)
 
 # Latest release deployed on cluster is a prerequisite, it is handled by deploy-latest-release target
diff --git a/README.md b/README.md
index 1215e0c365..904854c159 100644
--- a/README.md
+++ b/README.md
@@ -20,13 +20,19 @@ Kyma Istio Operator is a component of the Kyma runtime that handles the manageme
 
 ### Procedure
 
-1. To install Istio, you must install the latest version of Kyma Istio Operator and Istio CRD first. Run:
+1. Create the `kyma-system` namespace:
+
+   ```bash
+   kubectl create namespace kyma-system
+   ```
+
+2. To install Istio, you must install the latest version of Kyma Istio Operator and Istio CRD first. Run:
 
    ```bash
    kubectl apply -f https://github.com/kyma-project/istio/releases/latest/download/istio-manager.yaml
    ```
 
-2. To get Istio installed, apply the default Istio CR:
+3. To get Istio installed, apply the default Istio CR:
 
    ```bash
    kubectl apply -f https://github.com/kyma-project/istio/releases/latest/download/istio-default-cr.yaml
@@ -38,7 +44,7 @@ Kyma Istio Operator is a component of the Kyma runtime that handles the manageme
    istio.operator.kyma-project.io/default created
    ```
 
-3. Check the state of Istio CR to verify if Istio was installed successfully:
+4. Check the state of Istio CR to verify if Istio was installed successfully:
 
    ```bash
    kubectl get -n kyma-system istios/default
@@ -57,7 +63,7 @@ For more installation options, visit [the installation guide](/docs/contributor/
 
 To learn how to use Kyma Istio Operator, read the documentation in the [`user`](/docs/user) directory.
 
-If you are interested in the detailed documentation of the Kyma Istio Operator's design and technical aspects, check the [`contributor`](/docs/contributor/) directory.
+If you are interested in the detailed documentation of the Kyma Istio Operator's design and technical aspects, check the [`contributor`](/docs/contributor) directory.
 
 ## Contributing
 
diff --git a/config/manager/manager.yaml b/config/manager/manager.yaml
index 9c4ed899cf..e0305122fd 100644
--- a/config/manager/manager.yaml
+++ b/config/manager/manager.yaml
@@ -1,16 +1,3 @@
-apiVersion: v1
-kind: Namespace
-metadata:
-  labels:
-    control-plane: controller-manager
-    app.kubernetes.io/name: namespace
-    app.kubernetes.io/instance: system
-    app.kubernetes.io/component: manager
-    app.kubernetes.io/created-by: istio
-    app.kubernetes.io/part-of: istio
-    app.kubernetes.io/managed-by: kustomize
-  name: system
----
 apiVersion: apps/v1
 kind: Deployment
 metadata: