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Helm vs Kustomize in GitOps – Which One to Choose?
Govardhana M K
October 09, 2025
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🧠 DEEP DIVE USE CASE
Helm vs Kustomize in GitOps – Which One to Choose?
When teams start with GitOps, the first debate isn’t about tools. It’s about structure.
Do you keep everything in a single repository?
Do you separate configurations by environment or by cluster?
Do you maintain different repos for access control or team boundaries?
These are the questions that define your GitOps repository strategy, commonly known as Monorepo vs Polyrepo.
Monorepo
Everything sits in one place. The base manifests, the environment overlays, and even Helm values.
It feels simple at the start. One pull request can roll out a change across multiple clusters.
But over time, reviews get messy. Teams touch the same files. Access control becomes tricky. One wrong merge can trigger a production sync you didn’t plan for.
Polyrepo
Each app or environment has its own repository.
It gives clear boundaries and better ownership. Teams can deploy and roll back without waiting on others. But the price you pay is coordination. Keeping shared components like ingress or policies in sync across repos takes effort.
Most setups I’ve worked on end up somewhere in between. A central repo for cluster-wide components. Separate repos for app or environment configs.
When Helm and Kustomize Coexist in GitOps
In real GitOps setups, both Helm and Kustomize often appear together because of how repositories, applications, and cluster environments evolve over time.
Helm usually enters first, it’s the default choice when teams start adopting GitOps. Many third-party tools ship as Helm charts, and controllers like Argo CD or Flux can deploy them directly from chart repositories.
Kustomize often gets introduced later. Once teams need to manage multiple clusters or environments, they use overlays to patch Helm-rendered outputs or to combine different components into a single deployment view.
At that point, the two coexist naturally. A single Argo CD instance may track dozens of Helm releases and multiple Kustomize overlays in parallel. Some apps are deployed directly from Helm charts, while others reference Helm outputs through resources: inside kustomization.yaml.
With this basic real world production reality lens, let’s get into how each works, the GitOps repo directory structure, and which one to choose.
How Helm Works ?
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