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The way to do this is currently to patch the Operator deployment like this:

patches:
- patch: |
    apiVersion: apps/v1
    kind: Deployment
    metadata:
      name: controller-manager
    spec:
      template:
        spec:
          containers:
          - name: manager
            env:
              - name: PULL_SECRET
                value: pull-secret
  target:
    kind: Deployment
    name: controller-manager

Setting the PULL_SECRET variable on the operator deployment will add the pull secret to all the workloads deployed by the operator

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Answer selected by pvbiesen
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