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Even with a minimal kustomization.yaml, Kustomize lets you orchestrate Kubernetes manifests across many folders—no extra scripting required.

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Flat Directory Structure

When you start small, a single directory often suffices: 
k8s/
├── api-depl.yaml
├── api-service.yaml
├── db-depl.yaml
└── db-service.yaml
To deploy all resources at once: 
kubectl apply -f k8s/
This is plain Kubernetes—no Kustomize features yet.

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Introducing Subdirectories

As your manifest count grows, you might split them: 
k8s/
├── api/
│   ├── api-depl.yaml
│   └── api-service.yaml
└── db/
    ├── db-depl.yaml
    └── db-service.yaml
Now deployment requires two commands: 
kubectl apply -f k8s/api/
kubectl apply -f k8s/db/
Manually running kubectl apply in each subfolder can be error-prone and difficult to automate in CI/CD.

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Single Root kustomization.yaml

Instead of listing directories every time, create a single kustomization.yaml at k8s/: 
apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization

resources:
  - api/api-depl.yaml
  - api/api-service.yaml
  - db/db-depl.yaml
  - db/db-service.yaml
Then deploy with one of these commands: 
kustomize build k8s/ | kubectl apply -f -
# or
kubectl apply -k k8s/
kubectl apply -k invokes Kustomize natively—you don’t need the standalone binary.

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When the Resource List Grows

Adding more services (e.g., cache/, kafka/) quickly makes the root manifest unwieldy: 
k8s/
├── api/
├── db/
├── cache/
│   ├── redis-config.yaml
│   ├── redis-depl.yaml
│   └── redis-service.yaml
└── kafka/
    ├── kafka-config.yaml
    ├── kafka-depl.yaml
    └── kafka-service.yaml
A flat list of ten or more files in one kustomization.yaml is hard to maintain.

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Nested kustomization.yaml Files

A cleaner pattern is to give each subdirectory its own kustomization.yaml: k8s/api/kustomization.yaml 
apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization

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

resources:
  - db-depl.yaml
  - db-service.yaml
Repeat for cache/ and kafka/. Then simplify your root kustomization.yaml: 
apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization

resources:
  - api/
  - db/
  - cache/
  - kafka/
Deploy everything in one go: 
kubectl apply -k k8s/
# or
kustomize build k8s/ | kubectl apply -f -
This hierarchical layout keeps the root file concise and scales seamlessly.

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Command Reference

LayoutCommand
Flat folderkubectl apply -f k8s/
Single-root Kustomizationkubectl apply -k k8s/
Build then applykustomize build k8s/ | kubectl apply -f -

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