In your prometheus.yml file, make sur you use pod for the role when setting up the kubernetes_sd_configs.

- job_name: 'kubernetes-pods'

  kubernetes_sd_configs:
  - role: pod

  relabel_configs:
  # only scrape when annotation prometheus.io/scrape: 'true' is set
  - source_labels: [__meta_kubernetes_pod_annotation_prometheus_io_scrape]
    action: keep
    regex: true
  - source_labels: [__meta_kubernetes_pod_annotation_prometheus_io_path]
    action: replace
    target_label: __metrics_path__
    regex: (.+)
  - source_labels: [__address__, __meta_kubernetes_pod_annotation_prometheus_io_port]
    action: replace
    regex: (.+):(?:\d+);(\d+)
    replacement: ${1}:${2}
    target_label: __address__
  - action: labelmap
    regex: __meta_kubernetes_pod_label_(.+)
  - source_labels: [__meta_kubernetes_namespace]
    action: replace
    target_label: kubernetes_namespace
  - source_labels: [__meta_kubernetes_pod_name]
    action: replace
    target_label: kubernetes_pod_name

and add the proper annotations to your Deployment config:

kind: Deployment

...

spec:
  template:
    metadata:
      annotations:
        prometheus.io/scrape: "true"
        prometheus.io/port: "<< PORT OF YOUR CONTAINER >>"

Source