Case Study – Managing Directories with and without Kustomize

Sometimes we only want to organize multiple Kubernetes manifests into a single directory and deploy them together, without adding overlays, patches, or transformers. This is where Kustomize’s Managing Directories feature is useful.

In this case study, we will explore different approaches for managing directories, starting from plain Kubernetes commands (without Kustomize) and then moving to more structured setups with Kustomize.

1. Without Kustomize

Option A – Apply Files One by One

If you only have a few manifests, you can directly apply them individually:

kubectl apply -f api-deploy.yaml
kubectl apply -f api-service.yaml
kubectl apply -f db-deploy.yaml
kubectl apply -f db-service.yaml

This works, but quickly becomes unmanageable when the number of files increases.

Option B – Apply a Directory

Instead of applying files one by one, you can place all manifests inside a single directory and apply them together:

my-app/
├── api-deploy.yaml
├── api-service.yaml
├── db-deploy.yaml
└── db-service.yaml

Now you can run:

kubectl apply -f ./my-app

This applies all manifests in the directory at once. However, this approach has limitations — you cannot easily manage different environments (staging, prod, etc.) or modularize the structure.

controlplane ~ ➜  tree code/k8s/
code/k8s/
├── db
│   ├── db-config.yaml
│   ├── db-depl.yaml
│   └── db-service.yaml
├── message-broker
│   ├── rabbitmq-config.yaml
│   ├── rabbitmq-depl.yaml
│   └── rabbitmq-service.yaml
└── nginx
    ├── nginx-depl.yaml
    └── nginx-service.yaml

3 directories, 8 files

controlplane ~ ➜  k apply -f code/k8s/
error: error reading [code/k8s/]: recognized file extensions are [.json .yaml .yml]

controlplane ~ ✖ k apply -f code/k8s/db/
configmap/db-credentials created
deployment.apps/db-deployment created
service/db-service created

controlplane ~ ➜  k apply -f code/k8s/message-broker/
configmap/redis-credentials created
deployment.apps/rabbitmq-deployment created
service/rabbit-cluster-ip-service created

controlplane ~ ➜  k apply -f code/k8s/nginx/
deployment.apps/nginx-deployment created
service/nginx-service created

2. With Kustomize

Kustomize provides two ways to manage manifests more efficiently.

Option A – Single kustomization.yaml in a Directory

You create a single kustomization.yaml that lists all resources:

my-app/
├── api-deploy.yaml
├── api-service.yaml
├── db-deploy.yaml
├── db-service.yaml
└── kustomization.yaml

kustomization.yaml

resources:
  - api-deploy.yaml
  - api-service.yaml
  - db-deploy.yaml
  - db-service.yaml

Deploy with:

kubectl apply -k ./my-app

This already improves maintainability by making deployments declarative and reusable.

controlplane ~ ➜  touch code/k8s/kustomization.yaml

controlplane ~ ➜  vi code/k8s/kustomization.yaml

controlplane ~ ➜  k apply -k code/k8s
error: accumulating resources: accumulation err='accumulating resources from 'db/': '/root/code/k8s/db' must resolve to a file': couldn't make target for path '/root/code/k8s/db': unable to find one of 'kustomization.yaml', 'kustomization.yml' or 'Kustomization' in directory '/root/code/k8s/db'

controlplane ~ ✖ cat code/k8s/kustomization.yaml
apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
resources:
  - db/
  - message-broker/
  - nginx/

controlplane ~ ➜  vi code/k8s/kustomization.yaml

controlplane ~ ➜  k apply -k code/k8s
configmap/db-credentials unchanged
configmap/redis-credentials unchanged
service/db-service unchanged
service/nginx-service unchanged
service/rabbit-cluster-ip-service unchanged
deployment.apps/db-deployment unchanged
deployment.apps/nginx-deployment unchanged
deployment.apps/rabbitmq-deployment unchanged

controlplane ~ ➜  cat code/k8s/kustomization.yaml
apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
resources:
  - db/db-config.yaml
  - db/db-depl.yaml
  - db/db-service.yaml
  - message-broker/rabbitmq-config.yaml
  - message-broker/rabbitmq-depl.yaml
  - message-broker/rabbitmq-service.yaml
  - nginx/nginx-depl.yaml
  - nginx/nginx-service.yaml

Option B – Nested kustomization.yaml (Modular / Pro Version)

As the app grows, you may want to organize resources into sub-directories, each with its own kustomization.yaml. Then a top-level file combines them.

Directory structure:

my-app/
├── api/
│   ├── api-deploy.yaml
│   ├── api-service.yaml
│   └── kustomization.yaml
├── db/
│   ├── db-deploy.yaml
│   ├── db-service.yaml
│   └── kustomization.yaml
└── kustomization.yaml   # top-level

api/kustomization.yaml

resources:
  - api-deploy.yaml
  - api-service.yaml

db/kustomization.yaml

resources:
  - db-deploy.yaml
  - db-service.yaml

top-level kustomization.yaml

resources:
  - ./api
  - ./db

Deploy everything with:

kubectl apply -k ./my-app

controlplane ~ ➜  cat > code/k8s/db/kustomization.yaml
apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
resources:
 - db-config.yaml
 - db-depl.yaml
 - db-service.yaml

controlplane ~ ➜  cat > code/k8s/message-broker/kustomization.yaml
apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
resources:
 - rabbitmq-config.yaml
 - rabbitmq-depl.yaml
 - rabbitmq-service.yaml

controlplane ~ ➜  cat > code/k8s/nginx/kustomization.yaml
apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
resources:
 - nginx-depl.yaml
 - nginx-service.yaml

controlplane ~ ➜  cat > code/k8s/kustomization.yaml
apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
resources:
  - db/
  - message-broker/
  - nginx/ 

controlplane ~ ➜  k apply -k code/k8s
configmap/db-credentials unchanged
configmap/redis-credentials unchanged
service/db-service unchanged
service/nginx-service unchanged
service/rabbit-cluster-ip-service unchanged
deployment.apps/db-deployment unchanged
deployment.apps/nginx-deployment unchanged
deployment.apps/rabbitmq-deployment unchanged

controlplane ~ ➜  tree code/k8s/
code/k8s/
├── db
│   ├── db-config.yaml
│   ├── db-depl.yaml
│   ├── db-service.yaml
│   └── kustomization.yaml
├── kustomization.yaml
├── message-broker
│   ├── kustomization.yaml
│   ├── rabbitmq-config.yaml
│   ├── rabbitmq-depl.yaml
│   └── rabbitmq-service.yaml
└── nginx
    ├── kustomization.yaml
    ├── nginx-depl.yaml
    └── nginx-service.yaml

3 directories, 12 files

controlplane ~ ➜

Conclusion

  • Without Kustomize:

  • You can either apply manifests one by one or apply an entire directory at once.

  • With Kustomize:

  • You can manage manifests more systematically using kustomization.yaml.

  • Either put all manifests under one kustomization.yaml or go modular with sub-directories for better scalability.

This layered approach makes it easier to maintain, scale, and manage different environments in Kubernetes.