diff --git a/CHANGELOG.next.asciidoc b/CHANGELOG.next.asciidoc
index 525d234afd6..21e6e83e863 100644
--- a/CHANGELOG.next.asciidoc
+++ b/CHANGELOG.next.asciidoc
@@ -90,6 +90,7 @@ https://github.com/elastic/beats/compare/v7.0.0-alpha2...master[Check the HEAD d
 - Fix merging of fileset inputs to replace paths and append processors. {pull}16450{16450}
 - Add queue_url definition in manifest file for aws module. {pull}16640{16640}
 - Fix issue where autodiscover hints default configuration was not being copied. {pull}16987[16987]
+- Fix Elasticsearch `_id` field set by S3 and Google Pub/Sub inputs. {pull}17026[17026]
 
 *Heartbeat*
 
diff --git a/x-pack/filebeat/input/googlepubsub/input.go b/x-pack/filebeat/input/googlepubsub/input.go
index f2b5811e194..e9f48073d74 100644
--- a/x-pack/filebeat/input/googlepubsub/input.go
+++ b/x-pack/filebeat/input/googlepubsub/input.go
@@ -193,25 +193,24 @@ func makeTopicID(project, topic string) string {
 func makeEvent(topicID string, msg *pubsub.Message) beat.Event {
 	id := topicID + "-" + msg.ID
 
-	fields := common.MapStr{
-		"event": common.MapStr{
-			"id":      id,
-			"created": time.Now().UTC(),
+	event := beat.Event{
+		Timestamp: msg.PublishTime.UTC(),
+		Fields: common.MapStr{
+			"event": common.MapStr{
+				"id":      id,
+				"created": time.Now().UTC(),
+			},
+			"message": string(msg.Data),
 		},
-		"message": string(msg.Data),
+		Private: msg,
 	}
+	event.SetID(id)
+
 	if len(msg.Attributes) > 0 {
-		fields.Put("labels", msg.Attributes)
+		event.PutValue("labels", msg.Attributes)
 	}
 
-	return beat.Event{
-		Timestamp: msg.PublishTime.UTC(),
-		Meta: common.MapStr{
-			"id": id,
-		},
-		Fields:  fields,
-		Private: msg,
-	}
+	return event
 }
 
 func (in *pubsubInput) getOrCreateSubscription(ctx context.Context, client *pubsub.Client) (*pubsub.Subscription, error) {
diff --git a/x-pack/filebeat/input/s3/input.go b/x-pack/filebeat/input/s3/input.go
index d75499b4d11..d10ea10bd63 100644
--- a/x-pack/filebeat/input/s3/input.go
+++ b/x-pack/filebeat/input/s3/input.go
@@ -587,33 +587,34 @@ func (p *s3Input) deleteMessage(queueURL string, messagesReceiptHandle string, s
 }
 
 func createEvent(log string, offset int, info s3Info, objectHash string, s3Ctx *s3Context) beat.Event {
-	f := common.MapStr{
-		"message": log,
-		"log": common.MapStr{
-			"offset":    int64(offset),
-			"file.path": constructObjectURL(info),
-		},
-		"aws": common.MapStr{
-			"s3": common.MapStr{
-				"bucket": common.MapStr{
-					"name": info.name,
-					"arn":  info.arn},
-				"object.key": info.key,
+	s3Ctx.Inc()
+
+	event := beat.Event{
+		Timestamp: time.Now().UTC(),
+		Fields: common.MapStr{
+			"message": log,
+			"log": common.MapStr{
+				"offset":    int64(offset),
+				"file.path": constructObjectURL(info),
+			},
+			"aws": common.MapStr{
+				"s3": common.MapStr{
+					"bucket": common.MapStr{
+						"name": info.name,
+						"arn":  info.arn},
+					"object.key": info.key,
+				},
+			},
+			"cloud": common.MapStr{
+				"provider": "aws",
+				"region":   info.region,
 			},
 		},
-		"cloud": common.MapStr{
-			"provider": "aws",
-			"region":   info.region,
-		},
+		Private: s3Ctx,
 	}
+	event.SetID(objectHash + "-" + fmt.Sprintf("%012d", offset))
 
-	s3Ctx.Inc()
-	return beat.Event{
-		Timestamp: time.Now(),
-		Fields:    f,
-		Meta:      common.MapStr{"id": objectHash + "-" + fmt.Sprintf("%012d", offset)},
-		Private:   s3Ctx,
-	}
+	return event
 }
 
 func constructObjectURL(info s3Info) string {