Short answer: put the annotations in your Kubernetes work pool’s base job template. That’s what the worker uses to create the Job/Pod for each flow run. Helm chart-level podAnnotations usually only affect the worker pod itself, not the flow-run pods. Two ways to apply annotations to the flow-run pods: 1) Update the work pool’s base job template (recommended) - Fetch the default template, add annotations under job_configuration.job_manifest.spec.template.metadata.annotations, then create/update the work pool.

# 1) Get the default template
prefect work-pool get-default-base-job-template --type kubernetes > base-job-template.json

# 2) Edit base-job-template.json — add annotations here:
{
  "job_configuration": {
    "job_manifest": {
      "apiVersion": "batch/v1",
      "kind": "Job",
      "metadata": {
        "generateName": "{{ name }}-",
        "labels": "{{ labels }}",
        "namespace": "{{ namespace }}"
      },
      "spec": {
        "template": {
          "metadata": {
            "annotations": {
              "<http://sidecar.istio.io/inject|sidecar.istio.io/inject>": "false",
              "<http://example.com/team|example.com/team>": "data-eng"
            }
          },
          "spec": {
            "serviceAccountName": "{{ service_account_name }}",
            "restartPolicy": "Never",
            "containers": [
              {
                "name": "prefect-job",
                "image": "{{ image }}",
                "imagePullPolicy": "{{ image_pull_policy }}",
                "env": "{{ env }}",
                "args": "{{ command }}"
              }
            ]
          }
        },
        "ttlSecondsAfterFinished": "{{ finished_job_ttl }}"
      }
    },
    "command": "{{ command }}",
    "env": "{{ env }}",
    "labels": "{{ labels }}",
    "name": "{{ name }}",
    "namespace": "{{ namespace }}",
    "cluster_config": "{{ cluster_config }}"
  },
  "variables": { }
}

# 3) Create or update the work pool with this template
prefect work-pool create "my-k8s-pool" --type kubernetes --base-job-template ./base-job-template.json --overwrite

Then point your Helm-installed worker at that work pool (e.g., via env var

PREFECT_WORK_POOL_NAME=my-k8s-pool

in your worker chart values). 2) If your Helm chart supports passing a base job template Some versions of the Prefect OSS worker chart allow provisioning or updating a work pool on startup. If you have fields like

workPool.create

,

workPool.name

, and

workPool.baseJobTemplate

, you can embed the same JSON from above directly in values.yaml so it’s applied when the worker starts:

workPool:
  create: true
  name: my-k8s-pool
  type: kubernetes
  baseJobTemplate: |
    {
      "job_configuration": {
        "job_manifest": {
          "apiVersion": "batch/v1",
          "kind": "Job",
          "metadata": { "generateName": "{{ name }}-", "labels": "{{ labels }}", "namespace": "{{ namespace }}" },
          "spec": {
            "template": {
              "metadata": {
                "annotations": {
                  "<http://sidecar.istio.io/inject|sidecar.istio.io/inject>": "false",
                  "<http://example.com/team|example.com/team>": "data-eng"
                }
              },
              "spec": {
                "serviceAccountName": "{{ service_account_name }}",
                "restartPolicy": "Never",
                "containers": [
                  { "name": "prefect-job", "image": "{{ image }}", "imagePullPolicy": "{{ image_pull_policy }}", "env": "{{ env }}", "args": "{{ command }}" }
                ]
              }
            },
            "ttlSecondsAfterFinished": "{{ finished_job_ttl }}"
          }
        },
        "command": "{{ command }}",
        "env": "{{ env }}",
        "labels": "{{ labels }}",
        "name": "{{ name }}",
        "namespace": "{{ namespace }}",
        "cluster_config": "{{ cluster_config }}"
      },
      "variables": { }
    }

Important distinction

- Worker pod annotations (often

podAnnotations

or

worker.podAnnotations

in the Helm chart) only annotate the worker Deployment/Pod. - Flow-run pods are created by the work pool’s base job template; annotate them under job_configuration.job_manifest.spec.template.metadata.annotations as shown above. Docs and references - Deploy a worker with Helm: Deploy a worker using Helm - Manage work pools and base job templates: Manage work pools - Kubernetes integration overview: Prefect Kubernetes integration - Prefect Helm charts repo: prefect-helm If you share which annotations you need (e.g., Istio, IRSA, Linkerd), I can tailor the exact template and, if needed, expose them as variables so you can override per-deployment.