Metricbeat supports templates for modules:

["source","yaml",subs="attributes"]
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metricbeat.autodiscover:
  providers:
    - type: kubernetes
      include_annotations: ["prometheus.io.scrape"]
      templates:
        - condition:
            contains:
              kubernetes.annotations.prometheus.io.scrape: "true"
          config:
            - module: prometheus
              metricsets: ["collector"]
              hosts: "${data.host}:{data.port}"
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This configuration launches a `prometheus` module for all containers of pods annotated `prometheus.io.scrape=true`.