diff --git a/CHANGELOG.next.asciidoc b/CHANGELOG.next.asciidoc
index 6d24690f04a..469f36912b0 100644
--- a/CHANGELOG.next.asciidoc
+++ b/CHANGELOG.next.asciidoc
@@ -392,6 +392,7 @@ field. You can revert this change by configuring tags for the module and omittin
 - Update fields.yml in the azure module, missing metrics field. {pull}20918[20918]
 - The `elasticsearch/index` metricset only requests wildcard expansion for hidden indices if the monitored Elasticsearch cluster supports it. {pull}20938[20938]
 - Disable Kafka metricsets based on Jolokia by default. They require a different configuration. {pull}20989[20989]
+- Handle missing counters in the application_pool metricset. {pull}21071[21071]
 
 *Packetbeat*
 
diff --git a/x-pack/metricbeat/module/iis/application_pool/application_pool.go b/x-pack/metricbeat/module/iis/application_pool/application_pool.go
index 508e7b465e0..9c92894fb29 100644
--- a/x-pack/metricbeat/module/iis/application_pool/application_pool.go
+++ b/x-pack/metricbeat/module/iis/application_pool/application_pool.go
@@ -84,7 +84,6 @@ func (m *MetricSet) Fetch(report mb.ReporterV2) error {
 			break
 		}
 	}
-
 	return nil
 }
 
diff --git a/x-pack/metricbeat/module/iis/application_pool/reader.go b/x-pack/metricbeat/module/iis/application_pool/reader.go
index c4285c270c0..32c0c2d7ec3 100644
--- a/x-pack/metricbeat/module/iis/application_pool/reader.go
+++ b/x-pack/metricbeat/module/iis/application_pool/reader.go
@@ -101,10 +101,10 @@ func (r *Reader) initAppPools() error {
 			if err == pdh.PDH_CSTATUS_NO_COUNTER || err == pdh.PDH_CSTATUS_NO_COUNTERNAME || err == pdh.PDH_CSTATUS_NO_INSTANCE || err == pdh.PDH_CSTATUS_NO_OBJECT {
 				r.log.Infow("Ignoring non existent counter", "error", err,
 					logp.Namespace("application pool"), "query", value)
-				continue
 			} else {
-				return errors.Wrapf(err, `failed to expand counter (query="%v")`, value)
+				r.log.Error(err, `failed to expand counter path (query= "%v")`, value)
 			}
+			continue
 		}
 		newQueries = append(newQueries, childQueries...)
 		// check if the pdhexpandcounterpath/pdhexpandwildcardpath functions have expanded the counter successfully.