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Understanding ArgoCD Reconciliation: How It Works, Why It Matters, and Best Practices

ArgoCD is a powerful GitOps controller for Kubernetes, enabling declarative configuration and automated synchronization of workloads. One of its core functions is reconciliation, a continuous process by which ArgoCD ensures that the live state of a Kubernetes cluster matches the desired state defined in a Git repository.

While this might sound straightforward, reconciliation plays a critical role in the GitOps lifecycle, and its default behavior can be surprisingly aggressive. In this blog post, we’ll explore:

  • What reconciliation in ArgoCD actually does
  • Why it exists and how it ensures cluster integrity
  • The pitfalls of the default timer
  • Best practices for tuning reconciliation to balance responsiveness and resource efficiency

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In a related blog, we describe how customers using Rafay are able to Block Drift in the first place.

ArgoCD Reconciliation

What Is Reconciliation in ArgoCD?

In simple terms, reconciliation is the process by which ArgoCD checks and ensures that the current state of resources deployed in the Kubernetes cluster matches the desired state stored in Git.

Every application managed by ArgoCD is periodically reconciled.

This means:

  1. ArgoCD fetches the target state from Git (or a Helm/Kustomize template if used).
  2. It compares that desired state with the current state in the cluster.
  3. If a difference is found—and automated sync is enabled—ArgoCD will attempt to bring the cluster back into alignment by applying necessary changes.

This loop is similar to how Kubernetes controllers work internally, but with Git as the source of truth instead of the Kubernetes API server.

Why Reconciliation Exists: Guardrails for GitOps

The reconciliation loop is vital for the GitOps model to succeed. Reconciliation ensures that Git remains the authoritative source of truth and minimizes human-induced configuration drift—one of the leading causes of production incidents in Kubernetes environments. Its key purposes are:

Drift Detection

If someone manually changes a resource (e.g., via kubectl edit or another deployment tool), reconciliation catches that and highlights it as a deviation from the declared Git source.

Self Healing

When auto-sync is enabled, ArgoCD doesn’t just detect the drift—it corrects it, restoring the state to what Git defines.

Visibility

Even if auto-sync is off, ArgoCD flags out-of-sync resources in the UI, enabling developers or SREs to intervene manually.

Default Reconciliation Behavior: Surprisingly Aggressive

ArgoCD uses a default reconciliation interval of 3 minutes. This means every three minutes, for every application, ArgoCD will checks the live cluster state against the Git-defined desired state—even if nothing has changed in Git. While this may seem harmless in small clusters, in production environments with hundreds of applications, this can quickly become overwhelming:

Common issues that platform teams encounter with the default interval are:

Issue Description
High API load Each reconciliation involves multiple Kubernetes API queries (and potentially Git queries if not cached properly). This can add up quickly, putting pressure on both the cluster and ArgoCD.
Excessive Git traffic If your Git server is private or has rate limits (e.g., GitHub API), frequent polling can trigger throttling or rate limit violations.
Noisy logs and alerts Repeated reconciliation attempts—even when no changes are detected—can clutter logs or monitoring dashboards.
Poor scalability In large environments, the aggressive interval can become a scalability bottleneck for ArgoCD’s controllers.

It is really important to realize that ArgoCD’s reconciliation is pull-based. As a result, it doesn’t react instantly to Git webhooks or cluster events by default. It simply polls every X minutes.

Best Practices for Managing Reconciliation Timers

Given these concerns, it’s essential to understand how to configure the reconciliation timer wisely. Described below are some best practices for tuning reconciliation intervals and using advanced mechanisms.

1. Use Git Webhooks for Push-Based Sync Triggers

While ArgoCD’s reconciliation loop is pull-based, it supports webhook triggers from Git providers (e.g., GitHub, GitLab, Bitbucket). These triggers prompt ArgoCD to re-sync as soon as a new commit lands.

Best practice: Configure Git webhooks for every repository used by ArgoCD apps. This allows you to extend the reconciliation timer while still getting near-instant responsiveness to Git changes.

2. Increase the Reconciliation Interval for Stable Apps

For applications that don’t change often or don’t require tight drift detection, increase the reconciliation interval using the argocd.argoproj.io/sync-options annotation or global settings.

metadata:
  annotations:
    argocd.argoproj.io/sync-options: "ReconcileAt=manual"

Or globally, use application.reconcileTimeout in the ArgoCD config map.

Recommendation: Bump from 3 minutes to 10–15 minutes for most apps; even higher (30–60 minutes) for stable infrastructure components.

3. Enable Resource-Level Drift Detection Smartly

For certain critical applications (e.g., security agents or network policy managers), you might want to keep the default aggressive reconciliation—but this should be a conscious choice. You can even go one step further and use resource hooks or sync waves to control the order and timing of deployments.

4. Use the ReconcileAt Annotation for On-Demand Syncs

Instead of periodic polling, you can use the ReconcileAt mechanism to trigger reconciliation programmatically by updating an annotation on the Application object. 

metadata:
  annotations:
    argocd.argoproj.io/reconcile-at: "2025-08-06T12:00:00Z"

Recommendation: This is ideal for automation pipelines or GitOps workflows that only require reconciliation after a confirmed commit.

5. Group Applications Logically to Tune Timers

Group applications into projects and apply reconciliation timer policies at the project level if your environment is large.

This allows certain environments (e.g., staging) to be reconciled aggressively while others (e.g., dev or infra) are treated more passively.

When to Stick With the Default Timer

Despite its potential for overuse, the default 3-minute timer is appropriate in some cases:

  1. Environments with high change velocity, where Git commits are frequent and changes must propagate fast.
  2. Highly regulated systems, where drift must be detected within minutes.
  3. Security-critical workloads, where even temporary manual changes could violate compliance or security rules.

It is critical that you apply the default setting selectively, not universally.

Final Thoughts: Drift Detection With Discipline

Reconciliation in ArgoCD is both a guardian and a scalpel. It protects the system’s integrity but must be wielded with precision. Out of the box, it errs on the side of aggression, but thoughtful tuning can drastically improve performance and scalability.

To summarize:

  • Reconciliation ensures Git and cluster state remain in sync.
  • The default 3-minute interval is often too aggressive for large deployments.
  • Webhooks, custom intervals, and ReconcileAt annotations provide fine-grained control.
  • Think of reconciliation as a guardrail, not a hammer.

By embracing these best practices, teams can unlock the full power of GitOps while keeping ArgoCD lean, efficient, and scalable.

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In the next blog, we will describe how some customers use ArgoCD together with Rafay's Zero Trust Kubectl for Application Deployments and Lifecycle Management spanning a fleet of Kubernetes clusters.