diff --git a/CHANGELOG.asciidoc b/CHANGELOG.asciidoc
index ab6993a57f0..0cd50ed40e8 100644
--- a/CHANGELOG.asciidoc
+++ b/CHANGELOG.asciidoc
@@ -74,6 +74,7 @@ https://github.com/elastic/beats/compare/v5.0.0...master[Check the HEAD diff]
 - Only load matching states into prospector to improve state handling {pull}2840[2840]
 - Reset all states ttl on startup to make sure it is overwritten by new config {pull}2840[2840]
 - Persist all states for files which fall under ignore_older to have consistent behaviour {pull}2859[2859]
+- Improve shutdown behaviour with large number of files. {pull}3035[3035]
 
 *Winlogbeat*
 
diff --git a/filebeat/prospector/prospector_log.go b/filebeat/prospector/prospector_log.go
index 29d3d09bbac..d7b868f385b 100644
--- a/filebeat/prospector/prospector_log.go
+++ b/filebeat/prospector/prospector_log.go
@@ -202,6 +202,13 @@ func (p *ProspectorLog) scan() {
 
 	for path, info := range p.getFiles() {
 
+		select {
+		case <-p.Prospector.done:
+			logp.Info("Scan aborted because prospector stopped.")
+			return
+		default:
+		}
+
 		logp.Debug("prospector", "Check file for harvesting: %s", path)
 
 		// Create new state for comparison
diff --git a/filebeat/tests/system/test_registrar.py b/filebeat/tests/system/test_registrar.py
index c2ea05abf14..1dc4967a0aa 100644
--- a/filebeat/tests/system/test_registrar.py
+++ b/filebeat/tests/system/test_registrar.py
@@ -1137,7 +1137,7 @@ def test_restart_state_reset_ttl(self):
 
         self.render_config_template(
             path=os.path.abspath(self.working_dir) + "/log/test.log",
-            clean_inactive="10s",
+            clean_inactive="20s",
             ignore_older="5s"
         )
         os.mkdir(self.working_dir + "/log/")
@@ -1159,28 +1159,29 @@ def test_restart_state_reset_ttl(self):
         # Check that ttl > 0 was set because of clean_inactive
         data = self.get_registry()
         assert len(data) == 1
-        assert data[0]["ttl"] == 10 * 1000 * 1000 * 1000
+        assert data[0]["ttl"] == 20 * 1000 * 1000 * 1000
 
-        # No config file which does not match the existing state
+        # New config file which does not match the existing clean_inactive
         self.render_config_template(
             path=os.path.abspath(self.working_dir) + "/log/test.log",
-            clean_inactive="20s",
+            clean_inactive="40s",
             ignore_older="5s",
         )
 
         filebeat = self.start_beat(output="filebeat2.log")
 
         # Wait until new state is written
+
         self.wait_until(
-            lambda: self.log_contains("Flushing spooler because of timeout. Events flushed: ", logfile="filebeat2.log"),
-            max_timeout=10)
+            lambda: self.log_contains("Flushing spooler because of timeout. Events flushed: ",
+            logfile="filebeat2.log"), max_timeout=10)
 
         filebeat.check_kill_and_wait()
 
         # Check that ttl was reset correctly
         data = self.get_registry()
         assert len(data) == 1
-        assert data[0]["ttl"] == 20 * 1000 * 1000 * 1000
+        assert data[0]["ttl"] == 40 * 1000 * 1000 * 1000
 
     def test_restart_state_reset_ttl_with_space(self):
         """
@@ -1190,7 +1191,7 @@ def test_restart_state_reset_ttl_with_space(self):
 
         self.render_config_template(
             path=os.path.abspath(self.working_dir) + "/log/test file.log",
-            clean_inactive="10s",
+            clean_inactive="20s",
             ignore_older="5s"
         )
         os.mkdir(self.working_dir + "/log/")
@@ -1212,12 +1213,12 @@ def test_restart_state_reset_ttl_with_space(self):
         # Check that ttl > 0 was set because of clean_inactive
         data = self.get_registry()
         assert len(data) == 1
-        assert data[0]["ttl"] == 10 * 1000 * 1000 * 1000
+        assert data[0]["ttl"] == 20 * 1000 * 1000 * 1000
 
         # new config file whith other clean_inactive
         self.render_config_template(
             path=os.path.abspath(self.working_dir) + "/log/test file.log",
-            clean_inactive="20s",
+            clean_inactive="40s",
             ignore_older="5s",
         )
 
@@ -1233,7 +1234,7 @@ def test_restart_state_reset_ttl_with_space(self):
         # Check that ttl was reset correctly
         data = self.get_registry()
         assert len(data) == 1
-        assert data[0]["ttl"] == 20 * 1000 * 1000 * 1000
+        assert data[0]["ttl"] == 40 * 1000 * 1000 * 1000
 
 
     def test_restart_state_reset_ttl_no_clean_inactive(self):
diff --git a/filebeat/tests/system/test_shutdown.py b/filebeat/tests/system/test_shutdown.py
index 062354361b9..836e8fd6f97 100644
--- a/filebeat/tests/system/test_shutdown.py
+++ b/filebeat/tests/system/test_shutdown.py
@@ -42,7 +42,7 @@ def test_shutdown_wait_ok(self):
 
         # Wait until first flush
         self.wait_until(
-            lambda: self.log_contains("Flushing spooler because spooler full"),
+            lambda: self.log_contains_count("Flushing spooler") > 1,
             max_timeout=15)
 
         filebeat.check_kill_and_wait()