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The Kustomize Controller is the Flux component that ensures your cluster’s actual state matches the desired state described by Kubernetes manifests. It retrieves artifacts from the Source Controller and then:
FeatureDescription
ValidationChecks your manifests against the Kubernetes API before applying changes.
Apply / UpdateCreates or updates resources based on the desired state.
Health AssessmentMonitors workloads to ensure they remain healthy after deployment.
Pruning (Garbage Collection)Optionally removes resources that no longer exist in your source manifests.
Make sure you have installed Flux and configured a GitRepository or other supported source.

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1. Creating a Kustomization

Use the flux create kustomization command to link your source to a path containing Kustomize overlays. You can also enable garbage collection: 
flux create kustomization kustomization-app1 \
  --source=GitRepository/source-app1 \
  --path=./solar-system \
  --prune=true \
  --export > kustomization.yaml
The --export flag prints the Kustomization resource manifest: 
apiVersion: kustomize.toolkit.fluxcd.io/v1beta2
kind: Kustomization
metadata:
  name: kustomization-app1
  namespace: flux-system
spec:
  interval: 1m0s
  path: ./solar-system
  prune: true
  sourceRef:
    kind: GitRepository
    name: source-app1
Apply it with: 
kubectl apply -f kustomization.yaml

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2. Automatic Build Behavior

If there’s no kustomization.yaml file under ./solar-system, Flux will auto-generate one for you: 
kustomize create --autodetect --recursive --output kustomization.yaml
This populates kustomization.yaml with all discovered resources: 
apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
resources:
  - deployment.yaml
  - service.yaml
You don’t need to run the above command yourself—Flux performs it automatically when needed.

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3. Providing Your Own Overlays

If you include a custom kustomization.yaml (or Kustomization overlay) in the specified path, the controller will skip auto-generation and apply your overlays directly. This allows you to:
  • Add labels or annotations
  • Patch existing resources
  • Customize namespace or image tags

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4. Checking Status

To inspect all active Kustomization resources and their reconciliation state: 
flux get kustomizations
Example output: 
NAME                   REVISION          SUSPENDED   READY   MESSAGE
flux-system            main/7e35674...   False       True    Applied revision: 'main/7e35674...'
kustomization-app1     main/1b31558...   False       True    Applied revision: 'main/1b31558...'

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