diff --git a/cmd/kube-scheduler/app/options/configfile.go b/cmd/kube-scheduler/app/options/configfile.go
index ea0c9644271..384e86fb480 100644
--- a/cmd/kube-scheduler/app/options/configfile.go
+++ b/cmd/kube-scheduler/app/options/configfile.go
@@ -87,30 +87,6 @@ func LogOrWriteConfig(fileName string, cfg *config.KubeSchedulerConfiguration, c
 	}
 	cfg.Profiles = completedProfiles
 
-	if len(fileName) > 0 {
-		// Since the default component config lists all the default plugins as enabled
-		// without disabling them, we must explicitly disable all the plugins for each
-		// extension point using the "*" expression to ensure that the generated config
-		// file is usable
-		disabledPlugins := []config.Plugin{{Name: "*"}}
-		for i := range cfg.Profiles {
-			if cfg.Profiles[i].Plugins == nil {
-				continue
-			}
-			cfg.Profiles[i].Plugins.QueueSort.Disabled = disabledPlugins
-			cfg.Profiles[i].Plugins.PreFilter.Disabled = disabledPlugins
-			cfg.Profiles[i].Plugins.Filter.Disabled = disabledPlugins
-			cfg.Profiles[i].Plugins.PostFilter.Disabled = disabledPlugins
-			cfg.Profiles[i].Plugins.PreScore.Disabled = disabledPlugins
-			cfg.Profiles[i].Plugins.Score.Disabled = disabledPlugins
-			cfg.Profiles[i].Plugins.Reserve.Disabled = disabledPlugins
-			cfg.Profiles[i].Plugins.Permit.Disabled = disabledPlugins
-			cfg.Profiles[i].Plugins.PreBind.Disabled = disabledPlugins
-			cfg.Profiles[i].Plugins.Bind.Disabled = disabledPlugins
-			cfg.Profiles[i].Plugins.PostBind.Disabled = disabledPlugins
-		}
-	}
-
 	buf, err := encodeConfig(cfg)
 	if err != nil {
 		return err
diff --git a/pkg/scheduler/apis/config/v1beta2/default_plugins.go b/pkg/scheduler/apis/config/v1beta2/default_plugins.go
index 7eaa358143f..1d63003aa8b 100644
--- a/pkg/scheduler/apis/config/v1beta2/default_plugins.go
+++ b/pkg/scheduler/apis/config/v1beta2/default_plugins.go
@@ -156,6 +156,8 @@ type pluginIndex struct {
 func mergePluginSet(defaultPluginSet, customPluginSet v1beta2.PluginSet) v1beta2.PluginSet {
 	disabledPlugins := sets.NewString()
 	enabledCustomPlugins := make(map[string]pluginIndex)
+	// replacedPluginIndex is a set of index of plugins, which have replaced the default plugins.
+	replacedPluginIndex := sets.NewInt()
 	for _, disabledPlugin := range customPluginSet.Disabled {
 		disabledPlugins.Insert(disabledPlugin.Name)
 	}
@@ -170,16 +172,22 @@ func mergePluginSet(defaultPluginSet, customPluginSet v1beta2.PluginSet) v1beta2
 			}
 			// The default plugin is explicitly re-configured, update the default plugin accordingly.
 			if customPlugin, ok := enabledCustomPlugins[defaultEnabledPlugin.Name]; ok {
-				klog.InfoS("Defaut plugin is explicitly re-configured and is overriding.", "plugin", defaultEnabledPlugin.Name)
-				// update the default plugin in place to preserve order
+				klog.InfoS("Default plugin is explicitly re-configured; overriding", "plugin", defaultEnabledPlugin.Name)
+				// Update the default plugin in place to preserve order.
 				defaultEnabledPlugin = customPlugin.plugin
-				// kick the plugin from the enabled list of custom plugins
-				customPluginSet.Enabled = append(customPluginSet.Enabled[:customPlugin.index], customPluginSet.Enabled[customPlugin.index+1:]...)
+				replacedPluginIndex.Insert(customPlugin.index)
 			}
 			enabledPlugins = append(enabledPlugins, defaultEnabledPlugin)
 		}
 	}
 
-	enabledPlugins = append(enabledPlugins, customPluginSet.Enabled...)
+	// Append all the custom plugins which haven't replaced any default plugins.
+	// Note: duplicated custom plugins will still be appended here.
+	// If so, the instantiation of scheduler framework will detect it and abort.
+	for index, plugin := range customPluginSet.Enabled {
+		if !replacedPluginIndex.Has(index) {
+			enabledPlugins = append(enabledPlugins, plugin)
+		}
+	}
 	return v1beta2.PluginSet{Enabled: enabledPlugins}
 }
diff --git a/pkg/scheduler/apis/config/v1beta2/default_plugins_test.go b/pkg/scheduler/apis/config/v1beta2/default_plugins_test.go
index 417fa0a8a4d..934588833d7 100644
--- a/pkg/scheduler/apis/config/v1beta2/default_plugins_test.go
+++ b/pkg/scheduler/apis/config/v1beta2/default_plugins_test.go
@@ -367,6 +367,7 @@ func TestMergePlugins(t *testing.T) {
 				Filter: v1beta2.PluginSet{
 					Enabled: []v1beta2.Plugin{
 						{Name: "Plugin1", Weight: pointer.Int32Ptr(2)},
+						{Name: "Plugin3", Weight: pointer.Int32Ptr(3)},
 					},
 				},
 			},
@@ -374,6 +375,8 @@ func TestMergePlugins(t *testing.T) {
 				Filter: v1beta2.PluginSet{
 					Enabled: []v1beta2.Plugin{
 						{Name: "Plugin1"},
+						{Name: "Plugin2"},
+						{Name: "Plugin3"},
 					},
 				},
 			},
@@ -381,6 +384,8 @@ func TestMergePlugins(t *testing.T) {
 				Filter: v1beta2.PluginSet{
 					Enabled: []v1beta2.Plugin{
 						{Name: "Plugin1", Weight: pointer.Int32Ptr(2)},
+						{Name: "Plugin2"},
+						{Name: "Plugin3", Weight: pointer.Int32Ptr(3)},
 					},
 				},
 			},
@@ -391,6 +396,38 @@ func TestMergePlugins(t *testing.T) {
 				Filter: v1beta2.PluginSet{
 					Enabled: []v1beta2.Plugin{
 						{Name: "Plugin2", Weight: pointer.Int32Ptr(2)},
+						{Name: "Plugin1", Weight: pointer.Int32Ptr(1)},
+					},
+				},
+			},
+			defaultPlugins: &v1beta2.Plugins{
+				Filter: v1beta2.PluginSet{
+					Enabled: []v1beta2.Plugin{
+						{Name: "Plugin1"},
+						{Name: "Plugin2"},
+						{Name: "Plugin3"},
+					},
+				},
+			},
+			expectedPlugins: &v1beta2.Plugins{
+				Filter: v1beta2.PluginSet{
+					Enabled: []v1beta2.Plugin{
+						{Name: "Plugin1", Weight: pointer.Int32Ptr(1)},
+						{Name: "Plugin2", Weight: pointer.Int32Ptr(2)},
+						{Name: "Plugin3"},
+					},
+				},
+			},
+		},
+		{
+			name: "RepeatedCustomPlugin",
+			customPlugins: &v1beta2.Plugins{
+				Filter: v1beta2.PluginSet{
+					Enabled: []v1beta2.Plugin{
+						{Name: "Plugin1"},
+						{Name: "Plugin2", Weight: pointer.Int32Ptr(2)},
+						{Name: "Plugin3"},
+						{Name: "Plugin2", Weight: pointer.Int32Ptr(4)},
 					},
 				},
 			},
@@ -407,8 +444,9 @@ func TestMergePlugins(t *testing.T) {
 				Filter: v1beta2.PluginSet{
 					Enabled: []v1beta2.Plugin{
 						{Name: "Plugin1"},
-						{Name: "Plugin2", Weight: pointer.Int32Ptr(2)},
+						{Name: "Plugin2", Weight: pointer.Int32Ptr(4)},
 						{Name: "Plugin3"},
+						{Name: "Plugin2", Weight: pointer.Int32Ptr(2)},
 					},
 				},
 			},