diff --git a/CHANGELOG.asciidoc b/CHANGELOG.asciidoc
index 6c9a3c4513af..a9b5be4e9922 100644
--- a/CHANGELOG.asciidoc
+++ b/CHANGELOG.asciidoc
@@ -31,6 +31,7 @@ https://github.com/elastic/beats/compare/v6.0.0-alpha1...master[Check the HEAD d
 - Fix importing the dashboards when the limit for max open files is too low. {issue}4244[4244]
 
 *Filebeat*
+- Fix race condition on harvester stopping with reloading enabled. {issue}3779[3779]
 
 *Heartbeat*
 
diff --git a/filebeat/harvester/registry.go b/filebeat/harvester/registry.go
index 4b840e663640..08c0a20336cd 100644
--- a/filebeat/harvester/registry.go
+++ b/filebeat/harvester/registry.go
@@ -11,56 +11,69 @@ type Registry struct {
 	sync.RWMutex
 	harvesters map[uuid.UUID]Harvester
 	wg         sync.WaitGroup
+	done       chan struct{}
 }
 
 // NewRegistry creates a new registry object
 func NewRegistry() *Registry {
 	return &Registry{
 		harvesters: map[uuid.UUID]Harvester{},
+		done:       make(chan struct{}),
 	}
 }
 
-func (hr *Registry) add(h Harvester) {
-	hr.Lock()
-	defer hr.Unlock()
-	hr.harvesters[h.ID()] = h
-}
-
-func (hr *Registry) remove(h Harvester) {
-	hr.Lock()
-	defer hr.Unlock()
-	delete(hr.harvesters, h.ID())
+func (r *Registry) remove(h Harvester) {
+	r.Lock()
+	defer r.Unlock()
+	delete(r.harvesters, h.ID())
 }
 
 // Stop stops all harvesters in the registry
-func (hr *Registry) Stop() {
-	hr.Lock()
-	for _, hv := range hr.harvesters {
-		hr.wg.Add(1)
+func (r *Registry) Stop() {
+	r.Lock()
+	defer func() {
+		r.Unlock()
+		r.WaitForCompletion()
+	}()
+	// Makes sure no new harvesters are added during stopping
+	close(r.done)
+
+	for _, hv := range r.harvesters {
+		r.wg.Add(1)
 		go func(h Harvester) {
-			hr.wg.Done()
+			r.wg.Done()
 			h.Stop()
 		}(hv)
 	}
-	hr.Unlock()
-	hr.WaitForCompletion()
+
 }
 
 // WaitForCompletion can be used to wait until all harvesters are stopped
-func (hr *Registry) WaitForCompletion() {
-	hr.wg.Wait()
+func (r *Registry) WaitForCompletion() {
+	r.wg.Wait()
 }
 
 // Start starts the given harvester and add its to the registry
-func (hr *Registry) Start(h Harvester) {
+func (r *Registry) Start(h Harvester) {
+
+	// Make sure stop is not called during starting a harvester
+	r.Lock()
+	defer r.Unlock()
+
+	// Make sure no new harvesters are started after stop was called
+	select {
+	case <-r.done:
+		return
+	default:
+	}
 
-	hr.wg.Add(1)
-	hr.add(h)
+	r.wg.Add(1)
+	r.harvesters[h.ID()] = h
 
 	go func() {
 		defer func() {
-			hr.remove(h)
-			hr.wg.Done()
+			r.remove(h)
+			r.wg.Done()
 		}()
 		// Starts harvester and picks the right type. In case type is not set, set it to default (log)
 		h.Start()
@@ -68,8 +81,8 @@ func (hr *Registry) Start(h Harvester) {
 }
 
 // Len returns the current number of harvesters in the registry
-func (hr *Registry) Len() uint64 {
-	hr.RLock()
-	defer hr.RUnlock()
-	return uint64(len(hr.harvesters))
+func (r *Registry) Len() uint64 {
+	r.RLock()
+	defer r.RUnlock()
+	return uint64(len(r.harvesters))
 }