diff --git a/datadog_checks_base/datadog_checks/base/checks/prometheus/base_check.py b/datadog_checks_base/datadog_checks/base/checks/prometheus/base_check.py
index 64fc5a3babc1f..81286821beb54 100644
--- a/datadog_checks_base/datadog_checks/base/checks/prometheus/base_check.py
+++ b/datadog_checks_base/datadog_checks/base/checks/prometheus/base_check.py
@@ -146,6 +146,8 @@ def get_scraper(self, instance):
                 metrics_mapper[metric] = metric
             else:
                 metrics_mapper.update(metric)
+        # update metrics mapper with values provided by user
+        metrics_mapper.update(instance.get("metrics_mapper", {}))
 
         scraper.metrics_mapper = metrics_mapper
         scraper.labels_mapper = default_instance.get("labels_mapper", {})