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Organizing and scaling your Kubernetes manifests becomes much simpler when you adopt a consistent directory structure and leverage Kustomize. In this guide, we’ll walk through:
  • Defining a clear directory layout
  • Deploying resources manually with kubectl
  • Introducing Kustomize for centralized and per-directory customization

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Directory Layout

Under the k8s/ folder, structure your manifests by component: 
k8s/
├── api/
├── cache/
└── db/
DirectoryComponents
k8s/apiAPI Deployment & Service
k8s/cacheRedis Deployment, Service & Credentials
k8s/dbMongoDB Deployment, Service & Credentials
Each subfolder contains the YAML files for its service.

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Sample Manifests

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Database Deployment (db/db-depl.yaml)

apiVersion: apps/v1
kind: Deployment
metadata:
  name: db-deployment
spec:
  replicas: 1
  selector:
    matchLabels:
      component: db
  template:
    metadata:
      labels:
        component: db
    spec:
      containers:
      - name: mongo
        image: mongo
        env:
        - name: MONGO_INITDB_ROOT_USERNAME
          valueFrom:
            configMapKeyRef:
              name: db-credentials
              key: username
        - name: MONGO_INITDB_ROOT_PASSWORD
          valueFrom:
            configMapKeyRef:
              name: db-credentials
              key: password

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Redis Service (cache/redis-service.yaml)

apiVersion: v1
kind: Service
metadata:
  name: redis-cluster-ip-service
spec:
  type: ClusterIP
  selector:
    component: redis
  ports:
  - port: 6379
    targetPort: 6379

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Redis Credentials (cache/redis-config.yaml)

apiVersion: v1
kind: ConfigMap
metadata:
  name: redis-credentials
data:
  username: "redis"
  password: "password123"

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Manual Deployment

Apply each directory in sequence: 
kubectl apply -f k8s/api
kubectl apply -f k8s/cache
kubectl apply -f k8s/db
Or chain them: 
kubectl apply -f k8s/api -f k8s/cache -f k8s/db
Make sure your kubectl context is pointed to the correct cluster and you have permission to create resources.

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Cleaning Up

kubectl delete -f k8s/api -f k8s/cache -f k8s/db

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Introducing Kustomize

Kustomize lets you define and compose resources without template syntax. Start by creating a root kustomization.yaml under k8s/: 
apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
resources:
  - api/api-depl.yaml
  - api/api-service.yaml
  - cache/redis-config.yaml
  - cache/redis-depl.yaml
  - cache/redis-service.yaml
  - db/db-config.yaml
  - db/db-depl.yaml
  - db/db-service.yaml
Generate the merged manifest: 
kustomize build k8s/
Apply directly to the cluster: 
kustomize build k8s/ | kubectl apply -f -
Or use kubectl’s built-in Kustomize support:
You can apply overlays without installing the standalone Kustomize binary by running:
kubectl apply -k k8s/
See [Kubectl apply documentation].
Verify your pods: 
kubectl get pods

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Per-Directory Kustomization

For better modularity, place a kustomization.yaml in each subfolder.

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api/kustomization.yaml

apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
resources:
  - api-depl.yaml
  - api-service.yaml

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cache/kustomization.yaml

apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
resources:
  - redis-config.yaml
  - redis-depl.yaml
  - redis-service.yaml

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db/kustomization.yaml

apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
resources:
  - db-config.yaml
  - db-depl.yaml
  - db-service.yaml
Finally, update the root kustomization.yaml to reference directories: 
apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
resources:
  - api/
  - cache/
  - db/
Apply all components in one command: 
kubectl apply -k k8s/
Confirm everything is running: 
kubectl get pods
This scalable structure keeps your manifests organized and ready for production-grade overlays.

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