Helm vs Kustomize: We Manage 100+ Clusters - Here's What We Actually Use (2026)

Every Kubernetes team eventually hits the same question: should we use Helm, Kustomize, or both? After managing over 100 production clusters across financial services, healthcare, e-commerce, and SaaS organisations, we have a clear answer — it depends on the problem you are solving, and more often than not, the right answer is both.

This is not a theoretical overview. We are going to walk through architecture differences, the Helm 4 release (November 2025), real performance numbers, hybrid integration patterns, and a practical decision framework drawn from what we actually deploy in the field. If you are evaluating these tools or rethinking your current setup, this guide will save you weeks of trial and error.

How Helm and Kustomize Work: Architecture Fundamentals

Understanding the core architecture is essential before comparing features, because Helm and Kustomize solve the configuration problem from fundamentally different angles.

Helm: Templating and Package Management

Helm is the de facto package manager for Kubernetes. It uses Go templates to generate Kubernetes manifests dynamically. You define a chart — a directory containing templates, default values, metadata, and optional dependencies — and then customise it by passing different values.yaml files for each environment.

A simplified Helm workflow looks like this:

1. Write templates with Go template syntax ({{ .Values.replicaCount }})
2. Define defaults in values.yaml
3. Override values per environment (values-prod.yaml, values-staging.yaml)
4. Run helm install or helm upgrade to render templates and apply them to the cluster
5. Helm tracks the release history, enabling rollback with a single command

The CNCF graduated Helm in 2020, and it has since become the standard for distributing Kubernetes applications. With over 10,000 public charts on Artifact Hub and contributions from more than 1,600 organisations — including Google, Microsoft, IBM, and Datadog — Helm’s ecosystem is unmatched.

The trade-off is complexity. Go templates can become difficult to read and maintain. Conditionals, loops, and nested helper functions in _helpers.tpl files create an abstraction layer that obscures the actual YAML being generated. We have seen teams spend more time debugging template rendering than writing the manifests themselves.

Kustomize: Overlays and Pure YAML

Kustomize takes the opposite approach. There are no templates. Instead, you write plain Kubernetes YAML as your base configuration, then apply patches and overlays to modify it for different environments. Kustomize has been built into kubectl since Kubernetes 1.14, so there is nothing extra to install.

A typical Kustomize structure looks like this:

app/
  base/
    deployment.yaml
    service.yaml
    kustomization.yaml
  overlays/
    dev/
      kustomization.yaml
      replica-patch.yaml
    production/
      kustomization.yaml
      resource-patch.yaml

Each overlay references the base and applies targeted patches — strategic merge patches, JSON patches, or simple field replacements. The output is always deterministic, readable YAML. You run kubectl apply -k overlays/production/ or kustomize build overlays/production/ | kubectl apply -f - and you get exactly what you expect.

The advantage is transparency. Every configuration change is visible in plain YAML, which makes code reviews straightforward and aligns naturally with GitOps workflows. The disadvantage is that Kustomize has no concept of packaging, versioning, or release management. It does not track what was deployed or provide rollback. You need external tools — such as ArgoCD or Flux — to fill those gaps.

Helm 4: What Changed in November 2025

Helm 4 was released at KubeCon North America 2025 in Atlanta, marking the first major version update in six years. For teams already invested in Helm, this release addresses several long-standing pain points.

Server-Side Apply

Helm 4 now natively supports server-side apply, moving the apply logic from the client to the Kubernetes API server. This resolves conflict detection issues that plagued Helm 3 when multiple controllers managed the same resources. In our clusters, server-side apply eliminated the “last writer wins” problem that caused silent configuration drift during rolling updates.

WASM Plugin System

The new plugin architecture supports WebAssembly (WASM) plugins, making them portable across operating systems and CPU architectures. This is a significant improvement over Helm 3’s plugin system, which relied on OS-specific binaries. We expect the community to produce far more plugins now that distribution is no longer a barrier.

Embeddable SDK

Helm 4 allows its functionality to be embedded directly into other applications through an embeddable command SDK. Platform engineering teams can now build Helm into their internal developer portals and self-service platforms without shelling out to the Helm binary.

Chart API Evolution

Helm 4 lays the groundwork for new chart features without breaking backwards compatibility. Existing Helm 3 charts continue to work, but the new API enables future enhancements during the Helm 4 lifecycle. Security fixes are guaranteed until November 2026.

For teams planning upgrades, the migration from Helm 3 to 4 is relatively smooth — there are no equivalent of the Tiller removal that made the Helm 2 to 3 transition painful. We have already migrated a dozen client clusters to Helm 4 without incident.

Feature Comparison: Head to Head

Here is how Helm and Kustomize compare across the dimensions that matter most in production:

Feature	Helm	Kustomize
Approach	Templating (Go templates)	Overlay/patching (pure YAML)
Packaging	Charts with versioning and dependencies	No packaging — plain files
Distribution	Chart repositories, OCI registries, Artifact Hub	Git repositories only
Rollback	Built-in release history and helm rollback	No built-in rollback — requires external tools
Hooks	Pre/post install, upgrade, delete hooks	No hooks — use external pipeline logic
Testing	helm test with test pods	No built-in testing
Dependency management	Chart dependencies with version constraints	No dependency management
Learning curve	Steeper — Go templates, chart structure, release concepts	Gentler — plain YAML with overlay concepts
Native kubectl integration	No — requires separate binary	Yes — built into kubectl since 1.14
GitOps fit	Good with helm template in pipelines	Excellent — plain YAML diffs in Git
Conditionals and loops	Full Go template logic	No conditionals — multiple overlay files instead
Secret management	Helm Secrets plugin, SOPS integration	External tools (SOPS, Sealed Secrets)
Ecosystem	10,000+ charts, 75% adoption (CNCF 2025)	Built into kubectl, growing community

The 2025 CNCF Annual Survey confirms Helm’s dominance as the preferred Kubernetes package manager at 75% adoption. Kustomize does not appear as a separate line item in the survey, but its integration into kubectl means it is available by default on every cluster — making direct adoption comparisons difficult.

Performance Benchmarks: What We Actually Measured

Performance rarely appears in competitor comparisons, but it matters when your CI/CD pipeline runs hundreds of deployments per day. Here is what we measured across our client environments:

Operation	Helm	Kustomize
Simple overlay / small chart (10-20 resources)	2-3 seconds	< 1 second
Medium chart (50 templates)	3-5 seconds	1-2 seconds
Large chart (100+ templates)	5-10 seconds	2-3 seconds
Complex value processing	2-5 seconds additional	N/A (no templating)
Large cluster apply (1,000+ objects)	30-60 seconds	5-10 seconds

Kustomize is consistently faster because it performs straightforward YAML patching without a templating engine. Helm’s Go template rendering adds overhead proportional to chart complexity. For most teams, the difference is negligible — a few seconds per deployment. But if you are running a platform with hundreds of microservices deploying multiple times per day, those seconds compound.

The real performance consideration is not rendering speed but operational overhead. Helm’s release tracking adds state that must be managed (stored as Kubernetes Secrets by default). In clusters with hundreds of releases, helm list and helm history queries can slow down noticeably, and the Secrets accumulate unless you configure --history-max.

When to Use Helm vs Kustomize vs Both

After years of implementing both tools across diverse organisations, we have developed a straightforward decision framework.

Choose Helm When You Need

• Third-party application deployment — Installing Prometheus, NGINX Ingress, cert-manager, or any application from the broader ecosystem. The chart already exists and is maintained by the vendor. Fighting this by writing raw manifests is wasted effort.
• Application distribution — If other teams or customers need to install your application, Helm charts are the standard packaging format. Versioning, dependencies, and upgrade paths are built in.
• Lifecycle management — Rollback, upgrade history, and hooks are essential for production workloads where you need to recover quickly from failed deployments.
• Complex parameterisation — When your application requires conditionals, loops, or deeply nested configuration logic that would require dozens of Kustomize overlays.

Choose Kustomize When You Need

• Environment-specific customisation — You have the same application running across dev, staging, and production with small differences in replicas, resource limits, or configuration values.
• Minimal abstraction — Your team prefers working with plain YAML and wants every configuration change visible in a Git diff without rendering templates first.
• GitOps-native workflows — Tools like ArgoCD and Flux work excellently with Kustomize because the desired state is always plain, deterministic YAML.
• Internal applications — Services your team owns and operates, where packaging and distribution are unnecessary overhead.

Choose Both When You Need

• Third-party charts with custom overrides — Install NGINX Ingress via Helm, then use Kustomize to apply organisation-specific patches (custom annotations, additional labels, sidecar injection).
• Platform engineering at scale — Helm for the application catalogue, Kustomize for environment promotion. This is the pattern we see most frequently in mature organisations.
• Multi-team governance — Central platform teams publish Helm charts with sensible defaults, application teams apply Kustomize overlays for their specific needs.

Hybrid Patterns: Using Helm and Kustomize Together

The “Helm vs Kustomize” framing is misleading. In practice, mature platform teams combine them. Here are the four hybrid patterns we deploy most frequently.

Pattern 1: Helm Template Piped to Kustomize Build

Render the Helm chart to static YAML, then apply Kustomize patches:

helm template my-release my-chart \
  --values values-base.yaml \
  --output-dir rendered/

kustomize build overlays/production/ | kubectl apply -f -

The kustomization.yaml in overlays/production/ references the rendered output as its base. This gives you Helm’s templating power with Kustomize’s surgical patching. The downside is you lose Helm’s release tracking and rollback capabilities.

Pattern 2: Kustomize helmCharts Field

Kustomize can invoke Helm as a subprocess using the helmCharts field in kustomization.yaml:

apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization

helmCharts:
  - name: nginx-ingress
    repo: https://kubernetes.github.io/ingress-nginx
    version: 4.11.0
    releaseName: ingress
    valuesFile: values.yaml

patches:
  - path: custom-annotations.yaml

Run with kustomize build --enable-helm . and Kustomize renders the chart, then applies your patches on top. The output is a single YAML manifest combining both. The --enable-helm flag is required for security reasons — it authorises Kustomize to execute a Helm subprocess.

Pattern 3: Helm Post-Renderer

Use Helm’s --post-renderer flag to pipe rendered output through Kustomize before applying:

helm upgrade --install my-release my-chart \
  --values values.yaml \
  --post-renderer ./kustomize-post-render.sh

Where kustomize-post-render.sh runs kustomize build. This preserves Helm’s full lifecycle management (release tracking, rollback, hooks) while still applying Kustomize patches. We recommend this pattern when you need the best of both worlds.

Pattern 4: ArgoCD Multi-Source Applications

ArgoCD multi-source applications let you combine Helm charts and Kustomize overlays in a single Application manifest. This is particularly powerful for teams already running ArgoCD for GitOps-driven delivery:

apiVersion: argoproj.io/v1alpha1
kind: Application
spec:
  sources:
    - repoURL: https://charts.example.com
      chart: my-app
      targetRevision: 2.1.0
      helm:
        valueFiles:
          - $values/envs/production/values.yaml
    - repoURL: https://github.com/org/config
      targetRevision: main
      ref: values

This keeps chart versions and environment-specific configuration in separate Git repositories, enabling independent release cadences for application code and environment configuration.

Kustomize Components: The Alpha Feature Worth Watching

Traditional Kustomize overlays work well for environment variants (dev, staging, production), but they struggle with cross-cutting features that need to be enabled or disabled independently — such as caching, database backends, or monitoring sidecars.

Kustomize Components, introduced in v3.7.0 as an alpha feature, solve this by providing reusable configuration modules that overlays can mix and match:

app/
  base/
    kustomization.yaml
  components/
    caching/
      kustomization.yaml
    monitoring/
      kustomization.yaml
  overlays/
    production/
      kustomization.yaml  # includes both components
    dev/
      kustomization.yaml  # includes only monitoring

Each component is declared with kind: Component in its kustomization.yaml and can be imported into any overlay. This brings Kustomize closer to Helm’s conditional logic without introducing a templating language.

Components are still in alpha and considered experimental in Flux, but we have used them successfully in several internal deployments. If your team avoids Helm specifically because of the templating complexity, components may provide enough flexibility to stay pure-Kustomize for longer.

Common Mistakes and Pitfalls

We have seen the same mistakes repeatedly across client engagements. Here are the most costly ones for each tool.

Helm Pitfalls

• Sprawling values files — A single values.yaml with 500+ lines becomes unmaintainable. Split values by concern (networking, resources, features) and use helm install --values with multiple files.
• Ignoring chart linting — Always run helm lint and helm template in CI before deploying. We have seen production outages caused by template rendering errors that would have been caught by basic linting.
• Not setting --history-max — Helm stores every release as a Kubernetes Secret. Without limits, clusters accumulate thousands of Secrets. Set --history-max 10 on every helm upgrade.
• Blindly trusting community charts — Charts from Artifact Hub vary wildly in quality. Always review templates, check the maintainer’s track record, and pin to specific versions.
• Skipping chart provenance — Helm supports chart signing with GPG. In regulated industries, unsigned charts should not reach production. Helm 4’s WASM plugin system makes provenance verification easier to integrate.

Kustomize Pitfalls

• Overlay explosion — Without discipline, teams create overlays for every minor variation, resulting in dozens of near-identical directories. Use components and shared patches to reduce duplication.
• Missing validation — Kustomize does not validate that the output YAML is valid Kubernetes. Pipe kustomize build through kubectl apply --dry-run=server in CI to catch errors early.
• Ignoring resource ordering — Kustomize applies resources in alphabetical order by default. Use the resources field in kustomization.yaml to control ordering when dependencies exist between resources.
• No rollback strategy — Since Kustomize has no built-in release management, ensure your GitOps controller (ArgoCD, Flux) is configured for automated rollback or that your Git workflow supports rapid reverts.
• Complex patching chains — Strategic merge patches can interact in unexpected ways when multiple patches target the same resource. Test patch combinations explicitly rather than assuming they compose cleanly.

Understanding these pitfalls is closely related to broader Kubernetes mistakes teams should avoid in production.

Migration Guidance

If you are switching between tools, here is what we have learned from guiding multiple migrations.

From Helm to Kustomize

1. Render existing charts — Use helm template to generate the static YAML for each environment
2. Clean up rendered output — Use kubectl-neat to remove cluster-specific metadata and status fields
3. Create base manifests — Extract the common configuration as your Kustomize base
4. Build overlays — Convert each values-*.yaml into environment-specific patches
5. Migrate release tracking — Move to a GitOps controller (ArgoCD, Flux) for deployment tracking and rollback

Expect 2-4 weeks per application, depending on chart complexity. The biggest challenge is converting Helm’s conditional logic into Kustomize overlay structures.

From Kustomize to Helm

1. Analyse base and overlays — Map each base resource to a Helm template
2. Create values.yaml — Convert overlay-specific patches into template variables
3. Implement conditionals — Translate overlay include/exclude patterns into Go template {{ if }} blocks
4. Test rendering — Verify helm template output matches original kustomize build output for each environment
5. Set up chart repository — Publish to an OCI registry or chart museum for distribution

Expect 3-6 weeks. The templating conversion is the most time-consuming step, especially for applications with intricate patching logic.

Our Recommendation

In most cases, migration is unnecessary. The hybrid patterns described above let you adopt both tools incrementally. Start with Helm for third-party applications and Kustomize for internal services, then converge on a hybrid pattern as your platform matures. This approach aligns well with the broader GitOps, Helm, and ArgoCD playbook we use across our engagements.

Adoption and Ecosystem: The Numbers

For teams making a strategic decision, ecosystem health matters as much as features:

• Helm: 75% adoption among Kubernetes users (CNCF 2025 Survey), CNCF graduated project since 2020, 10,000+ charts on Artifact Hub, contributions from 1,600+ organisations, Helm 4 released November 2025 with security support until November 2026.
• Kustomize: Built into kubectl since v1.14, maintained under kubernetes-sigs with 11,900+ GitHub stars, no separate installation required, native fit with GitOps tools.
• GitOps tools: 77% of Kubernetes users have adopted GitOps to some degree (CNCF 2025), and both ArgoCD and Flux support Helm and Kustomize natively — meaning your tool choice does not lock you out of either GitOps controller.

The broader cloud native ecosystem continues to grow rapidly, with 15.6 million cloud native developers globally and 82% of container users running Kubernetes in production. Both Helm and Kustomize are well-positioned to remain core tools in this ecosystem for years to come.

Quick Decision Framework

If you want a fast answer, use this flowchart:

1. Are you installing a third-party application? Use Helm. The chart already exists.
2. Are you distributing your application to other teams or customers? Use Helm. Charts are the standard packaging format.
3. Are you customising the same internal application across environments? Use Kustomize. Overlays are simpler and more transparent.
4. Do you need rollback and release tracking? Use Helm or ensure your GitOps controller provides equivalent functionality.
5. Are you installing third-party charts but need custom patches? Use both — Helm for installation, Kustomize for customisation.
6. Are you building a platform for multiple teams? Use both — Helm for the application catalogue, Kustomize for team-specific overlays.

There is no wrong answer here. Both tools are mature, well-maintained, and widely adopted. The wrong move is spending months debating when you could be shipping.

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Kubernetes Configuration Management That Scales

Getting Helm, Kustomize, and your deployment pipeline working together smoothly across multiple clusters and environments is not trivial — especially when you factor in security best practices, compliance requirements, and the need for reliable rollback.

Our team provides comprehensive Kubernetes consulting services to help you:

• Design your configuration management strategy with the right mix of Helm and Kustomize for your organisation’s size and complexity
• Implement GitOps pipelines with ArgoCD or Flux that integrate both tools seamlessly
• Migrate existing deployments from ad-hoc kubectl scripts to a structured, repeatable approach
• Optimise for scale across multi-cluster, multi-team environments with proper governance and self-service capabilities

We have done this across 100+ production clusters. We know what works and where the hidden pitfalls are.

Talk to our Kubernetes engineering team today