diff --git a/CHANGELOG.asciidoc b/CHANGELOG.asciidoc
index 1d2467d2643..c017a21c5b7 100644
--- a/CHANGELOG.asciidoc
+++ b/CHANGELOG.asciidoc
@@ -68,6 +68,7 @@ https://github.com/elastic/beats/compare/v6.4.0...master[Check the HEAD diff]
 - Do not panic when no tokenizer string is configured for a dissect processor. {issue}8895[8895]
 - Start autodiscover consumers before producers. {pull}7926[7926]
 - The setup command will not fail if no dashboard is available to import. {pull}8977[8977]
+- Fix central management configurations reload when a configuration is removed in Kibana. {issue}9010[9010]
 
 *Auditbeat*
 
diff --git a/libbeat/common/reload/reload.go b/libbeat/common/reload/reload.go
index 1f8b3ab4a73..0e6933889e3 100644
--- a/libbeat/common/reload/reload.go
+++ b/libbeat/common/reload/reload.go
@@ -110,6 +110,23 @@ func (r *Registry) MustRegisterList(name string, list ReloadableList) {
 	}
 }
 
+// GetRegisteredNames returns the list of names registered
+func (r *Registry) GetRegisteredNames() []string {
+	r.RLock()
+	defer r.RUnlock()
+	var names []string
+
+	for name := range r.confs {
+		names = append(names, name)
+	}
+
+	for name := range r.confsLists {
+		names = append(names, name)
+	}
+
+	return names
+}
+
 // GetReloadable returns the reloadable object with the given name, nil if not found
 func (r *Registry) GetReloadable(name string) Reloadable {
 	r.RLock()
diff --git a/libbeat/publisher/pipeline/controller.go b/libbeat/publisher/pipeline/controller.go
index 908f5619fdd..fb811893aa5 100644
--- a/libbeat/publisher/pipeline/controller.go
+++ b/libbeat/publisher/pipeline/controller.go
@@ -153,8 +153,10 @@ func makeWorkQueue() workQueue {
 func (c *outputController) Reload(cfg *reload.ConfigWithMeta) error {
 	outputCfg := common.ConfigNamespace{}
 
-	if err := cfg.Config.Unpack(&outputCfg); err != nil {
-		return err
+	if cfg != nil {
+		if err := cfg.Config.Unpack(&outputCfg); err != nil {
+			return err
+		}
 	}
 
 	output, err := loadOutput(c.beat, c.monitors, outputCfg)
diff --git a/x-pack/libbeat/management/manager.go b/x-pack/libbeat/management/manager.go
index 084418b2db5..9c494fd8996 100644
--- a/x-pack/libbeat/management/manager.go
+++ b/x-pack/libbeat/management/manager.go
@@ -181,9 +181,24 @@ func (cm *ConfigManager) fetch() bool {
 
 func (cm *ConfigManager) apply() {
 	configOK := true
+
+	missing := map[string]bool{}
+	for _, name := range cm.registry.GetRegisteredNames() {
+		missing[name] = true
+	}
+
+	// Reload configs
 	for _, b := range cm.cache.Configs {
 		err := cm.reload(b.Type, b.Blocks)
 		configOK = configOK && err == nil
+		missing[b.Type] = false
+	}
+
+	// Unset missing configs
+	for name := range missing {
+		if missing[name] {
+			cm.reload(name, []*api.ConfigBlock{})
+		}
 	}
 
 	if !configOK {
@@ -199,15 +214,20 @@ func (cm *ConfigManager) reload(t string, blocks []*api.ConfigBlock) error {
 
 	if obj := cm.registry.GetReloadable(t); obj != nil {
 		// Single object
-		if len(blocks) != 1 {
+		if len(blocks) > 1 {
 			err := fmt.Errorf("got an invalid number of configs for %s: %d, expected: 1", t, len(blocks))
 			cm.logger.Error(err)
 			return err
 		}
-		config, err := blocks[0].ConfigWithMeta()
-		if err != nil {
-			cm.logger.Error(err)
-			return err
+
+		var config *reload.ConfigWithMeta
+		var err error
+		if len(blocks) == 1 {
+			config, err = blocks[0].ConfigWithMeta()
+			if err != nil {
+				cm.logger.Error(err)
+				return err
+			}
 		}
 
 		if err := obj.Reload(config); err != nil {
diff --git a/x-pack/libbeat/management/manager_test.go b/x-pack/libbeat/management/manager_test.go
index a7985299cb1..39c3a1f9e51 100644
--- a/x-pack/libbeat/management/manager_test.go
+++ b/x-pack/libbeat/management/manager_test.go
@@ -100,3 +100,68 @@ func TestConfigManager(t *testing.T) {
 	manager.Stop()
 	os.Remove(paths.Resolve(paths.Data, "management.yml"))
 }
+
+func TestRemoveItems(t *testing.T) {
+	registry := reload.NewRegistry()
+	id, err := uuid.NewV4()
+	if err != nil {
+		t.Fatalf("error while generating id: %v", err)
+	}
+	accessToken := "footoken"
+	reloadable := reloadable{
+		reloaded: make(chan *reload.ConfigWithMeta, 1),
+	}
+	registry.MustRegister("test.blocks", &reloadable)
+
+	mux := http.NewServeMux()
+	i := 0
+	responses := []string{
+		// Initial load
+		`{"configuration_blocks":[{"type":"test.blocks","config":{"module":"apache2"}}]}`,
+
+		// Return no blocks
+		`{"configuration_blocks":[]}`,
+	}
+	mux.Handle("/", http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+		fmt.Fprintf(w, responses[i])
+		i++
+	}))
+
+	server := httptest.NewServer(mux)
+
+	c, err := api.ConfigFromURL(server.URL)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	config := &Config{
+		Enabled:     true,
+		Period:      100 * time.Millisecond,
+		Kibana:      c,
+		AccessToken: accessToken,
+	}
+
+	manager, err := NewConfigManagerWithConfig(config, registry, id)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	manager.Start()
+
+	// On first reload we will get apache2 module
+	config1 := <-reloadable.reloaded
+	assert.Equal(t, &reload.ConfigWithMeta{
+		Config: common.MustNewConfigFrom(map[string]interface{}{
+			"module": "apache2",
+		}),
+	}, config1)
+
+	// Get a nil config, even if the block is not part of the payload
+	config2 := <-reloadable.reloaded
+	var nilConfig *reload.ConfigWithMeta
+	assert.Equal(t, nilConfig, config2)
+
+	// Cleanup
+	manager.Stop()
+	os.Remove(paths.Resolve(paths.Data, "management.yml"))
+}