diff --git a/CHANGELOG.next.asciidoc b/CHANGELOG.next.asciidoc
index ce5edbb6cd4..5374b3ed8d7 100644
--- a/CHANGELOG.next.asciidoc
+++ b/CHANGELOG.next.asciidoc
@@ -40,6 +40,7 @@ https://github.com/elastic/beats/compare/v8.2.0\...main[Check the HEAD diff]
 
 - Expand fields in `decode_json_fields` if target is set. {issue}31712[31712] {pull}32010[32010]
 - Fix OS name reported by add_host_metadata on Windows 11. {issue}30833[30833] {pull}32259[32259]
+- Fix race condition when reloading runners {pull}32309[32309]
 
 *Auditbeat*
 
@@ -49,6 +50,7 @@ https://github.com/elastic/beats/compare/v8.2.0\...main[Check the HEAD diff]
 - Fix Cisco AMP rate limit and pagination. {pull}32030[32030]
 - Fix wrong state ID in states registry for awss3 s3 direct input. {pull}32164[32164]
 - cisco/asa: fix handling of user names when there are Security Group Tags present. {issue}32009[32009] {pull}32196[32196]
+- Fix race conditions when reloading input V2 and filestream input {pull}32309[32309]
 
 *Heartbeat*
 
diff --git a/filebeat/input/filestream/internal/input-logfile/input.go b/filebeat/input/filestream/internal/input-logfile/input.go
index b0c5bf1d810..25f9cdac630 100644
--- a/filebeat/input/filestream/internal/input-logfile/input.go
+++ b/filebeat/input/filestream/internal/input-logfile/input.go
@@ -81,6 +81,10 @@ func (inp *managedInput) Run(
 
 	inp.prospector.Run(ctx, sourceStore, hg)
 
+	// Notify the manager the input  has stopped, currently that is used to
+	// keep track of duplicated IDs
+	inp.manager.StopInput(inp.userID)
+
 	return nil
 }
 
diff --git a/filebeat/input/filestream/internal/input-logfile/manager.go b/filebeat/input/filestream/internal/input-logfile/manager.go
index e7aba23a20e..0161c935a9d 100644
--- a/filebeat/input/filestream/internal/input-logfile/manager.go
+++ b/filebeat/input/filestream/internal/input-logfile/manager.go
@@ -71,6 +71,7 @@ type InputManager struct {
 	store      *store
 	ackUpdater *updateWriter
 	ackCH      *updateChan
+	idsMux     sync.Mutex
 	ids        map[string]struct{}
 }
 
@@ -176,12 +177,14 @@ func (cim *InputManager) Create(config *conf.C) (v2.Input, error) {
 			" duplication, please add an ID and restart Filebeat")
 	}
 
+	cim.idsMux.Lock()
 	if _, exists := cim.ids[settings.ID]; exists {
 		cim.Logger.Errorf("filestream input with ID '%s' already exists, this "+
 			"will lead to data duplication, please use a different ID", settings.ID)
 	}
 
 	cim.ids[settings.ID] = struct{}{}
+	cim.idsMux.Unlock()
 
 	prospector, harvester, err := cim.Configure(config)
 	if err != nil {
@@ -226,6 +229,13 @@ func (cim *InputManager) Create(config *conf.C) (v2.Input, error) {
 	}, nil
 }
 
+// StopInput peforms all necessary clean up when an input finishes.
+func (cim *InputManager) StopInput(id string) {
+	cim.idsMux.Lock()
+	delete(cim.ids, id)
+	cim.idsMux.Unlock()
+}
+
 func (cim *InputManager) getRetainedStore() *store {
 	store := cim.store
 	store.Retain()
diff --git a/filebeat/input/v2/compat/compat.go b/filebeat/input/v2/compat/compat.go
index 32d89ae7ea0..146b7098994 100644
--- a/filebeat/input/v2/compat/compat.go
+++ b/filebeat/input/v2/compat/compat.go
@@ -104,11 +104,13 @@ func (f *factory) Create(
 func (r *runner) String() string { return r.input.Name() }
 
 func (r *runner) Start() {
+	r.wg.Add(1)
 	log := r.log
 	name := r.input.Name()
 
 	go func() {
-		log.Infof("Input %v starting", name)
+		defer r.wg.Done()
+		log.Infof("Input '%s' starting", name)
 		err := r.input.Run(
 			v2.Context{
 				ID:          r.id,
@@ -119,9 +121,9 @@ func (r *runner) Start() {
 			r.connector,
 		)
 		if err != nil {
-			log.Errorf("Input '%v' failed with: %+v", name, err)
+			log.Errorf("Input '%s' failed with: %+v", name, err)
 		} else {
-			log.Infof("Input '%v' stopped", name)
+			log.Infof("Input '%s' stopped (goroutine)", name)
 		}
 	}()
 }
@@ -129,7 +131,7 @@ func (r *runner) Start() {
 func (r *runner) Stop() {
 	r.sig.Cancel()
 	r.wg.Wait()
-	r.log.Infof("Input '%v' stopped", r.input.Name())
+	r.log.Infof("Input '%s' stopped (runner)", r.input.Name())
 }
 
 func configID(config *conf.C) (string, error) {
diff --git a/filebeat/tests/system/test_reload_inputs.py b/filebeat/tests/system/test_reload_inputs.py
index cfc5a2f8f5f..3daf7c8d9d4 100644
--- a/filebeat/tests/system/test_reload_inputs.py
+++ b/filebeat/tests/system/test_reload_inputs.py
@@ -281,11 +281,6 @@ def test_reload_same_config(self):
         with open(self.working_dir + "/configs/input.yml", 'w') as f:
             f.write(inputConfigTemplate.format(self.working_dir + "/logs/test.log"))
 
-        # Make sure error shows up in log file
-        self.wait_until(
-            lambda: self.log_contains("Can only start an input when all related states are finished"),
-            max_timeout=15)
-
         # Wait until old runner is stopped
         self.wait_until(
             lambda: self.log_contains("Stopping runner:"),
diff --git a/libbeat/cfgfile/list.go b/libbeat/cfgfile/list.go
index 88f2b2a5e26..76608bfd8e0 100644
--- a/libbeat/cfgfile/list.go
+++ b/libbeat/cfgfile/list.go
@@ -81,14 +81,23 @@ func (r *RunnerList) Reload(configs []*reload.ConfigWithMeta) error {
 
 	r.logger.Debugf("Start list: %d, Stop list: %d", len(startList), len(stopList))
 
+	wg := sync.WaitGroup{}
 	// Stop removed runners
 	for hash, runner := range stopList {
+		wg.Add(1)
 		r.logger.Debugf("Stopping runner: %s", runner)
 		delete(r.runners, hash)
-		go runner.Stop()
+		go func() {
+			defer wg.Done()
+			runner.Stop()
+			r.logger.Debugf("Runner: '%s' has stopped", runner)
+		}()
 		moduleStops.Add(1)
 	}
 
+	// Wait for all runners to stop before starting new ones
+	wg.Wait()
+
 	// Start new runners
 	for hash, config := range startList {
 		runner, err := createRunner(r.factory, r.pipeline, config)