diff --git a/.github/workflows/bootstrap.yaml b/.github/workflows/bootstrap.yaml
index afe26b7b..2d4a4f58 100644
--- a/.github/workflows/bootstrap.yaml
+++ b/.github/workflows/bootstrap.yaml
@@ -33,7 +33,7 @@ jobs:
         uses: fluxcd/pkg//actions/kustomize@main
       - name: Build
         run: |
-          make cmd/flux/manifests
+          make cmd/flux/.manifests.done
           go build -o /tmp/flux ./cmd/flux
       - name: Set outputs
         id: vars
diff --git a/.github/workflows/scan.yaml b/.github/workflows/scan.yaml
index 029a59a6..9e1cc45b 100644
--- a/.github/workflows/scan.yaml
+++ b/.github/workflows/scan.yaml
@@ -31,7 +31,7 @@ jobs:
         uses: fluxcd/pkg//actions/kustomize@main
       - name: Build manifests
         run: |
-          make cmd/flux/manifests
+          make cmd/flux/.manifests.done
       - name: Run Snyk to check for vulnerabilities
         uses: snyk/actions/golang@master
         continue-on-error: true
diff --git a/.gitignore b/.gitignore
index 0a385d36..c431bf85 100644
--- a/.gitignore
+++ b/.gitignore
@@ -19,6 +19,7 @@ dist/
 bin/
 output/
 cmd/flux/manifests/
+cmd/flux/.manifests.done
 
 # Docs
 site/
diff --git a/Makefile b/Makefile
index 6426e7a2..563a672b 100644
--- a/Makefile
+++ b/Makefile
@@ -1,5 +1,5 @@
 VERSION?=$(shell grep 'VERSION' cmd/flux/main.go | awk '{ print $$4 }' | head -n 1 | tr -d '"')
-EMBEDDED_MANIFESTS_TARGET=cmd/flux/manifests
+EMBEDDED_MANIFESTS_TARGET=cmd/flux/.manifests.done
 TEST_KUBECONFIG?=/tmp/flux-e2e-test-kubeconfig
 ENVTEST_BIN_VERSION?=latest
 KUBEBUILDER_ASSETS?="$(shell $(SETUP_ENVTEST) use -i $(ENVTEST_BIN_VERSION) -p path)"
@@ -46,6 +46,7 @@ test-with-kind: setup-envtest
 
 $(EMBEDDED_MANIFESTS_TARGET): $(call rwildcard,manifests/,*.yaml *.json)
 	./manifests/scripts/bundle.sh
+	touch $@
 
 build: $(EMBEDDED_MANIFESTS_TARGET)
 	CGO_ENABLED=0 go build -ldflags="-s -w -X main.VERSION=$(VERSION)" -o ./bin/flux ./cmd/flux