How can I add custom tolerations to managed EKS add-ons like CoreDNS and Metrics Server?

You’ll need to modify the managed add-on resources after they’re created. Since managed add-ons (like CoreDNS and Metrics Server) don’t offer a built‑in mechanism to override their tolerations via the EKS add-on configuration, you must patch their deployments (or DaemonSets) to add the appropriate tolerations.

For example, to add the “spotty” toleration to CoreDNS you can run a patch command like this:

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kubectl -n kube-system patch deployment coredns \
  --patch '{
    "spec": {
      "template": {
        "spec": {
          "tolerations": [
            {
              "key": "spotty",
              "operator": "Equal",
              "value": "true",
              "effect": "NoSchedule"
            }
          ]
        }
      }
    }
  }'

And similarly for Metrics Server (assuming its deployment is in the kube-system namespace and named “metrics-server”):

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kubectl -n kube-system patch deployment metrics-server \
  --patch '{
    "spec": {
      "template": {
        "spec": {
          "tolerations": [
            {
              "key": "spotty",
              "operator": "Equal",
              "value": "true",
              "effect": "NoSchedule"
            }
          ]
        }
      }
    }
  }'

Keep in mind that since these add-ons are managed by EKS, any future updates might override your changes. As such, you could automate this patching process (for example, using a post-deployment hook or a continuous delivery/automation tool) or monitor updates to reapply the patch when needed.