diff --git a/.github/workflows/bootstrap.yaml b/.github/workflows/bootstrap.yaml
index 2d4a4f58..74ed0ed0 100644
--- a/.github/workflows/bootstrap.yaml
+++ b/.github/workflows/bootstrap.yaml
@@ -64,6 +64,21 @@ jobs:
           --team=team-z
         env:
           GITHUB_TOKEN: ${{ secrets.GITPROVIDER_BOT_TOKEN }}
+      - name: bootstrap customize
+        run: |
+          make setup-bootstrap-patch
+          /tmp/flux bootstrap github --manifests ./manifests/install/ \
+          --owner=fluxcd-testing \
+          --repository=${{ steps.vars.outputs.test_repo_name }} \
+          --branch=main \
+          --path=test-cluster \
+          --team=team-z
+          if [ $(kubectl get deployments.apps source-controller -o jsonpath='{.spec.template.spec.securityContext.runAsUser}') != "10000" ]; then
+          echo "Bootstrap not customized as controller is not running as user 10000" && exit 1
+          fi
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITPROVIDER_BOT_TOKEN }}
+          GITHUB_REPO_NAME: ${{ steps.vars.outputs.test_repo_name }}
       - name: libgit2
         run: |
           /tmp/flux create source git test-libgit2 \
diff --git a/Makefile b/Makefile
index f6d168d0..631d2767 100644
--- a/Makefile
+++ b/Makefile
@@ -58,10 +58,12 @@ install:
 install-dev:
 	CGO_ENABLED=0 go build -o /usr/local/bin ./cmd/flux
 
-
 install-envtest:  setup-envtest
 	 $(SETUP_ENVTEST) use $(ENVTEST_BIN_VERSION)
 
+setup-bootstrap-patch:
+	go run ./tests/bootstrap/main.go
+
 # Find or download setup-envtest
 setup-envtest:
 ifeq (, $(shell which setup-envtest))
diff --git a/tests/bootstrap/main.go b/tests/bootstrap/main.go
new file mode 100644
index 00000000..e7735d8e
--- /dev/null
+++ b/tests/bootstrap/main.go
@@ -0,0 +1,81 @@
+package main
+
+import (
+	"context"
+	"log"
+	"os"
+
+	"github.com/fluxcd/go-git-providers/github"
+	"github.com/fluxcd/go-git-providers/gitprovider"
+)
+
+func main() {
+	ks := "test-cluster/flux-system/kustomization.yaml"
+	patchName := "test-cluster/flux-system/gotk-patches.yaml"
+	ksContent := `apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+resources:
+- gotk-components.yaml
+- gotk-sync.yaml
+patches:
+  - path: gotk-patches.yaml
+    target:
+      kind: Deployment`
+	patchContent := `apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: all-flux-components
+spec:
+  template:
+    metadata:
+      annotations:
+        # Required by Kubernetes node autoscaler
+        cluster-autoscaler.kubernetes.io/safe-to-evict: "true"
+    spec:
+      securityContext:
+        runAsUser: 10000
+        fsGroup: 1337
+      containers:
+        - name: manager
+          securityContext:
+            readOnlyRootFilesystem: true
+            allowPrivilegeEscalation: false
+            runAsNonRoot: true
+            capabilities:
+              drop:
+                - ALL
+`
+	commitFiles := []gitprovider.CommitFile{
+		{
+			Path:    &ks,
+			Content: &ksContent,
+		},
+		{
+			Path:    &patchName,
+			Content: &patchContent,
+		},
+	}
+	repoName := os.Getenv("GITHUB_REPO_NAME")
+	githubToken := os.Getenv("GITHUB_TOKEN")
+	client, err := github.NewClient(github.WithOAuth2Token(githubToken))
+	if err != nil {
+		log.Fatalf("error initializing github client: %s", err)
+	}
+
+	repoRef := gitprovider.OrgRepositoryRef{
+		OrganizationRef: gitprovider.OrganizationRef{
+			Organization: "flux-testing",
+			Domain:       "github.com",
+		},
+		RepositoryName: repoName,
+	}
+	repo, err := client.OrgRepositories().Get(context.Background(), repoRef)
+	if err != nil {
+		log.Fatalf("error getting %s repository in org %s: %s", repoRef.RepositoryName, repoRef.Organization, err)
+	}
+
+	_, err = repo.Commits().Create(context.Background(), "main", "add patch manifest 3", commitFiles)
+	if err != nil {
+		log.Fatalf("error making commit: %s", err)
+	}
+}