diff --git a/CHANGELOG.next.asciidoc b/CHANGELOG.next.asciidoc
index f4871d41df69..5e3a2efd0c83 100644
--- a/CHANGELOG.next.asciidoc
+++ b/CHANGELOG.next.asciidoc
@@ -30,6 +30,7 @@ https://github.com/elastic/beats/compare/v7.0.0-alpha2...master[Check the HEAD d
 - ILM will be available by default if Elasticsearch > 7.0 is used. {pull}10347[10347]
 - Allow Central Management to send events back to kibana. {issue}9382[9382]
 - Initialize the Paths before the keystore and save the keystore into `data/{beatname}.keystore`. {pull}10706[10706]
+- Add `cleanup_timeout` option to docker autodiscover, to wait some time before removing configurations after a container is stopped. {issue]10374[10374] {pull}10905[10905]
 
 *Auditbeat*
 
diff --git a/filebeat/tests/system/test_autodiscover.py b/filebeat/tests/system/test_autodiscover.py
index 973577920d33..c25ec9081024 100644
--- a/filebeat/tests/system/test_autodiscover.py
+++ b/filebeat/tests/system/test_autodiscover.py
@@ -23,6 +23,7 @@ def test_docker(self):
             inputs=False,
             autodiscover={
                 'docker': {
+                    'cleanup_timeout': '0s',
                     'templates': '''
                       - condition:
                           equals.docker.container.image: busybox
diff --git a/libbeat/autodiscover/providers/docker/config.go b/libbeat/autodiscover/providers/docker/config.go
index bba4f32cdb0c..1f3bae7aa5b4 100644
--- a/libbeat/autodiscover/providers/docker/config.go
+++ b/libbeat/autodiscover/providers/docker/config.go
@@ -18,6 +18,8 @@
 package docker
 
 import (
+	"time"
+
 	"github.com/elastic/beats/libbeat/autodiscover/template"
 	"github.com/elastic/beats/libbeat/common"
 	"github.com/elastic/beats/libbeat/common/docker"
@@ -34,13 +36,15 @@ type Config struct {
 	Appenders      []*common.Config        `config:"appenders"`
 	Templates      template.MapperSettings `config:"templates"`
 	Dedot          bool                    `config:"labels.dedot"`
+	CleanupTimeout time.Duration           `config:"cleanup_timeout"`
 }
 
 func defaultConfig() *Config {
 	return &Config{
-		Host:   "unix:///var/run/docker.sock",
-		Prefix: "co.elastic",
-		Dedot:  true,
+		Host:           "unix:///var/run/docker.sock",
+		Prefix:         "co.elastic",
+		Dedot:          true,
+		CleanupTimeout: 60 * time.Second,
 	}
 }
 
diff --git a/libbeat/autodiscover/providers/docker/docker.go b/libbeat/autodiscover/providers/docker/docker.go
index fb0901e55e51..f0c4d0438fa2 100644
--- a/libbeat/autodiscover/providers/docker/docker.go
+++ b/libbeat/autodiscover/providers/docker/docker.go
@@ -19,6 +19,7 @@ package docker
 
 import (
 	"errors"
+	"time"
 
 	"github.com/gofrs/uuid"
 
@@ -115,7 +116,9 @@ func (d *Provider) Start() {
 				d.emitContainer(event, "start")
 
 			case event := <-d.stopListener.Events():
-				d.emitContainer(event, "stop")
+				time.AfterFunc(d.config.CleanupTimeout, func() {
+					d.emitContainer(event, "stop")
+				})
 			}
 		}
 	}()
diff --git a/libbeat/autodiscover/providers/docker/docker_integration_test.go b/libbeat/autodiscover/providers/docker/docker_integration_test.go
index d790744aa489..ccba884df9ee 100644
--- a/libbeat/autodiscover/providers/docker/docker_integration_test.go
+++ b/libbeat/autodiscover/providers/docker/docker_integration_test.go
@@ -43,8 +43,9 @@ func TestDockerStart(t *testing.T) {
 		t.Fatal(err)
 	}
 	bus := bus.New("test")
-	config := common.NewConfig()
-	provider, err := AutodiscoverBuilder(bus, UUID, config)
+	config := defaultConfig()
+	config.CleanupTimeout = 0
+	provider, err := AutodiscoverBuilder(bus, UUID, common.MustNewConfigFrom(config))
 	if err != nil {
 		t.Fatal(err)
 	}
diff --git a/metricbeat/tests/system/test_autodiscover.py b/metricbeat/tests/system/test_autodiscover.py
index 1b41e80a1dfd..ae135a8f7fc5 100644
--- a/metricbeat/tests/system/test_autodiscover.py
+++ b/metricbeat/tests/system/test_autodiscover.py
@@ -23,6 +23,7 @@ def test_docker(self):
         self.render_config_template(
             autodiscover={
                 'docker': {
+                    'cleanup_timeout': '0s',
                     'templates': '''
                       - condition:
                           equals.docker.container.image: memcached:latest
@@ -69,6 +70,7 @@ def test_docker_labels(self):
         self.render_config_template(
             autodiscover={
                 'docker': {
+                    'cleanup_timeout': '0s',
                     'hints.enabled': 'true',
                 },
             },
@@ -111,6 +113,7 @@ def test_config_appender(self):
         self.render_config_template(
             autodiscover={
                 'docker': {
+                    'cleanup_timeout': '0s',
                     'hints.enabled': 'true',
                     'appenders': '''
                       - type: config