Bootstrap — install Flux and store its own config in Git

The bootstrap command does two things at once: installs Flux controllers in the cluster, and commits the Flux configuration to your Git repository. Flux then manages itself — it will update its own controllers when you change the config in Git.

# Install Flux CLI
brew install fluxcd/tap/flux   # macOS
curl -s https://fluxcd.io/install.sh | sudo bash  # Linux

# Bootstrap to GitHub — installs Flux AND commits config to Git
flux bootstrap github \
  --owner=myorg \
  --repository=fleet-infra \
  --branch=main \
  --path=clusters/production \
  --personal

# After bootstrap: Flux controllers run in flux-system namespace
# AND the Git repo has a flux-system/ folder with Flux config committed
kubectl get pods -n flux-system

Core Flux CRDs — the resources you create

# GitRepository — watch a repo every 1 minute
apiVersion: source.toolkit.fluxcd.io/v1
kind: GitRepository
metadata:
  name: payment-service
  namespace: flux-system
spec:
  interval: 1m
  url: https://github.com/company/payment-service
  ref:
    branch: main
---
# Kustomization — apply ./deploy folder from the GitRepository
apiVersion: kustomize.toolkit.fluxcd.io/v1
kind: Kustomization
metadata:
  name: payment-service
  namespace: flux-system
spec:
  interval: 5m
  path: ./deploy
  prune: true          # delete resources removed from Git
  sourceRef:
    kind: GitRepository
    name: payment-service
  targetNamespace: production

What is Kustomize?

Kustomize lets you customise Kubernetes YAML for different environments without templates or placeholders. You define base manifests once, then create per-environment overlays that patch specific fields. No Go template syntax — just plain Kubernetes YAML with structured patches.

Base + overlay directory structure

deploy/
├── base/
│   ├── kustomization.yaml     # lists base resources
│   ├── deployment.yaml        # base: 2 replicas, image tag = latest
│   └── service.yaml
└── overlays/
    ├── dev/
    │   └── kustomization.yaml # patch: 1 replica, dev namespace
    ├── staging/
    │   └── kustomization.yaml # patch: 3 replicas, staging namespace
    └── production/
        ├── kustomization.yaml # patch: 5 replicas, prod namespace
        └── resource-patch.yaml  # higher CPU/memory limits

# overlays/production/kustomization.yaml
apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
namespace: production
bases:
  - ../../base
images:
  - name: myapp
    newTag: v2.1.0        # override image tag for production
patchesStrategicMerge:
  - resource-patch.yaml  # patch CPU/memory limits

# overlays/production/resource-patch.yaml
apiVersion: apps/v1
kind: Deployment
metadata:
  name: payment-api
spec:
  replicas: 5
  template:
    spec:
      containers:
      - name: payment-api
        resources:
          requests: { cpu: "500m", memory: "512Mi" }
          limits:   { cpu: "2", memory: "2Gi" }

Kustomize vs Helm

What is image automation?

Image automation completes the CI/CD loop entirely within GitOps. When your CI pipeline builds and pushes a new image to ACR/ECR, Flux detects the new tag, selects it based on your policy, and commits the updated image tag back to Git automatically. Flux then applies that commit to the cluster — closing the loop without any human intervention.

# Step 1: Watch the container registry
apiVersion: image.toolkit.fluxcd.io/v1beta2
kind: ImageRepository
metadata:
  name: payment-api
  namespace: flux-system
spec:
  image: myacr.azurecr.io/payment-api
  interval: 5m
---
# Step 2: Policy — select latest semver tag
apiVersion: image.toolkit.fluxcd.io/v1beta2
kind: ImagePolicy
metadata:
  name: payment-api
  namespace: flux-system
spec:
  imageRepositoryRef:
    name: payment-api
  policy:
    semver:
      range: ">=1.0.0"
---
# Step 3: Mark the image line in your deployment.yaml
containers:
- name: payment-api
  image: myacr.azurecr.io/payment-api:v1.0.0 # {"$imagepolicy": "flux-system:payment-api"}
  # Flux replaces the tag automatically when a new version is published
---
# Step 4: Automation — commit the new tag back to Git
apiVersion: image.toolkit.fluxcd.io/v1beta1
kind: ImageUpdateAutomation
metadata:
  name: flux-system
  namespace: flux-system
spec:
  interval: 5m
  sourceRef:
    kind: GitRepository
    name: fleet-infra
  git:
    checkout:
      ref: { branch: main }
    commit:
      author:
        email: flux@company.com
        name: Flux
      messageTemplate: "chore: update image to {{range .Updated.Images}}{{println .}}{{end}}"
    push:
      branch: main