diff --git a/cmd/argocd/commands/app.go b/cmd/argocd/commands/app.go
index 25c02db5f291d..9f2a8295b60a5 100644
--- a/cmd/argocd/commands/app.go
+++ b/cmd/argocd/commands/app.go
@@ -137,13 +137,15 @@ func NewApplicationCreateCommand(clientOpts *argocdclient.ClientOptions) *cobra.
   # Create a Kustomize app
   argocd app create kustomize-guestbook --repo https://github.com/argoproj/argocd-example-apps.git --path kustomize-guestbook --dest-namespace default --dest-server https://kubernetes.default.svc --kustomize-image gcr.io/heptio-images/ks-guestbook-demo:0.1
 
+  # Create a MultiSource app while yaml file contains an application with multiple sources
+  argocd app create guestbook --file <path-to-yaml-file>
+
   # Create a app using a custom tool:
   argocd app create kasane --repo https://github.com/argoproj/argocd-example-apps.git --path plugins/kasane --dest-namespace default --dest-server https://kubernetes.default.svc --config-management-plugin kasane`,
 		Run: func(c *cobra.Command, args []string) {
 			ctx := c.Context()
 
 			argocdClient := headless.NewClientOrDie(clientOpts, c)
-
 			apps, err := cmdutil.ConstructApps(fileURL, appName, labels, annotations, args, appOpts, c.Flags())
 			errors.CheckError(err)
 
@@ -730,6 +732,7 @@ func NewApplicationSetCommand(clientOpts *argocdclient.ClientOptions) *cobra.Com
 	var (
 		appOpts      cmdutil.AppOptions
 		appNamespace string
+		sourceIndex  int
 	)
 	var command = &cobra.Command{
 		Use:   "set APPNAME",
@@ -747,6 +750,9 @@ func NewApplicationSetCommand(clientOpts *argocdclient.ClientOptions) *cobra.Com
   # Set and override application parameters with a parameter file
   argocd app set my-app --parameter-file path/to/parameter-file.yaml
 
+  # Set and override application parameters for a source at index 1 under spec.sources of app my-app. source-index starts at 1.
+  argocd app set my-app --source-index 1 --repo https://github.com/argoproj/argocd-example-apps.git
+
   # Set application parameters and specify the namespace
   argocd app set my-app --parameter key1=value1 --parameter key2=value2 --namespace my-namespace
   		`),
@@ -765,14 +771,25 @@ func NewApplicationSetCommand(clientOpts *argocdclient.ClientOptions) *cobra.Com
 			app, err := appIf.Get(ctx, &application.ApplicationQuery{Name: &appName, AppNamespace: &appNs})
 			errors.CheckError(err)
 
-			visited := cmdutil.SetAppSpecOptions(c.Flags(), &app.Spec, &appOpts)
+			if app.Spec.HasMultipleSources() {
+				if sourceIndex <= 0 {
+					errors.CheckError(fmt.Errorf("Source index should be specified and greater than 0 for applications with multiple sources"))
+				}
+				if len(app.Spec.GetSources()) < sourceIndex {
+					errors.CheckError(fmt.Errorf("Source index should be less than the number of sources in the application"))
+				}
+			}
+
+			// sourceIndex startes with 1, thus, it needs to be decreased by 1 to find the correct index in the list of sources
+			sourceIndex = sourceIndex - 1
+			visited := cmdutil.SetAppSpecOptions(c.Flags(), &app.Spec, &appOpts, sourceIndex)
 			if visited == 0 {
 				log.Error("Please set at least one option to update")
 				c.HelpFunc()(c, args)
 				os.Exit(1)
 			}
 
-			setParameterOverrides(app, appOpts.Parameters)
+			setParameterOverrides(app, appOpts.Parameters, sourceIndex)
 			_, err = appIf.UpdateSpec(ctx, &application.ApplicationUpdateSpecRequest{
 				Name:         &app.Name,
 				Spec:         &app.Spec,
@@ -782,6 +799,7 @@ func NewApplicationSetCommand(clientOpts *argocdclient.ClientOptions) *cobra.Com
 			errors.CheckError(err)
 		},
 	}
+	command.Flags().IntVar(&sourceIndex, "source-index", -1, "Index of the source from the list of sources of the app. Index starts at 1.")
 	cmdutil.AddAppFlags(command, &appOpts)
 	command.Flags().StringVarP(&appNamespace, "app-namespace", "N", "", "Set application parameters in namespace")
 	return command
@@ -801,6 +819,7 @@ type unsetOpts struct {
 	ignoreMissingValueFiles bool
 	pluginEnvs              []string
 	passCredentials         bool
+	ref                     bool
 }
 
 // IsZero returns true when the Application options for kustomize are considered empty
@@ -816,6 +835,9 @@ func (o *unsetOpts) KustomizeIsZero() bool {
 
 // NewApplicationUnsetCommand returns a new instance of an `argocd app unset` command
 func NewApplicationUnsetCommand(clientOpts *argocdclient.ClientOptions) *cobra.Command {
+	var (
+		sourceIndex int
+	)
 	appOpts := cmdutil.AppOptions{}
 	opts := unsetOpts{}
 	var appNamespace string
@@ -825,9 +847,12 @@ func NewApplicationUnsetCommand(clientOpts *argocdclient.ClientOptions) *cobra.C
 		Example: `  # Unset kustomize override kustomize image
   argocd app unset my-app --kustomize-image=alpine
 
-  # Unset kustomize override prefix
+  # Unset kustomize override suffix
   argocd app unset my-app --namesuffix
 
+  # Unset kustomize override suffix for source at index 1 under spec.sources of app my-app. source-index starts at 1.
+  argocd app unset my-app --source-index 1 --namesuffix
+
   # Unset parameter override
   argocd app unset my-app -p COMPONENT=PARAM`,
 
@@ -838,14 +863,25 @@ func NewApplicationUnsetCommand(clientOpts *argocdclient.ClientOptions) *cobra.C
 				c.HelpFunc()(c, args)
 				os.Exit(1)
 			}
+
 			appName, appNs := argo.ParseFromQualifiedName(args[0], appNamespace)
 			conn, appIf := headless.NewClientOrDie(clientOpts, c).NewApplicationClientOrDie()
 			defer argoio.Close(conn)
 			app, err := appIf.Get(ctx, &application.ApplicationQuery{Name: &appName, AppNamespace: &appNs})
 			errors.CheckError(err)
 
-			source := app.Spec.GetSource()
-			updated, nothingToUnset := unset(&source, opts)
+			if app.Spec.HasMultipleSources() {
+				if sourceIndex <= 0 {
+					errors.CheckError(fmt.Errorf("Source index should be specified and greater than 0 for applications with multiple sources"))
+				}
+				if len(app.Spec.GetSources()) < sourceIndex {
+					errors.CheckError(fmt.Errorf("Source index should be less than the number of sources in the application"))
+				}
+			}
+
+			source := app.Spec.GetSourcePtr(sourceIndex)
+
+			updated, nothingToUnset := unset(source, opts)
 			if nothingToUnset {
 				c.HelpFunc()(c, args)
 				os.Exit(1)
@@ -854,7 +890,7 @@ func NewApplicationUnsetCommand(clientOpts *argocdclient.ClientOptions) *cobra.C
 				return
 			}
 
-			cmdutil.SetAppSpecOptions(c.Flags(), &app.Spec, &appOpts)
+			cmdutil.SetAppSpecOptions(c.Flags(), &app.Spec, &appOpts, sourceIndex)
 			_, err = appIf.UpdateSpec(ctx, &application.ApplicationUpdateSpecRequest{
 				Name:         &app.Name,
 				Spec:         &app.Spec,
@@ -877,13 +913,22 @@ func NewApplicationUnsetCommand(clientOpts *argocdclient.ClientOptions) *cobra.C
 	command.Flags().StringArrayVar(&opts.kustomizeReplicas, "kustomize-replica", []string{}, "Kustomize replicas name (e.g. --kustomize-replica my-deployment --kustomize-replica my-statefulset)")
 	command.Flags().StringArrayVar(&opts.pluginEnvs, "plugin-env", []string{}, "Unset plugin env variables (e.g --plugin-env name)")
 	command.Flags().BoolVar(&opts.passCredentials, "pass-credentials", false, "Unset passCredentials")
+	command.Flags().BoolVar(&opts.ref, "ref", false, "Unset ref on the source")
+	command.Flags().IntVar(&sourceIndex, "source-index", -1, "Index of the source from the list of sources of the app. Index starts at 1.")
 	return command
 }
 
 func unset(source *argoappv1.ApplicationSource, opts unsetOpts) (updated bool, nothingToUnset bool) {
+	needToUnsetRef := false
+	if opts.ref && source.Ref != "" {
+		source.Ref = ""
+		updated = true
+		needToUnsetRef = true
+	}
+
 	if source.Kustomize != nil {
 		if opts.KustomizeIsZero() {
-			return false, true
+			return updated, !needToUnsetRef
 		}
 
 		if opts.namePrefix && source.Kustomize.NamePrefix != "" {
@@ -933,7 +978,7 @@ func unset(source *argoappv1.ApplicationSource, opts unsetOpts) (updated bool, n
 	}
 	if source.Helm != nil {
 		if len(opts.parameters) == 0 && len(opts.valuesFiles) == 0 && !opts.valuesLiteral && !opts.ignoreMissingValueFiles && !opts.passCredentials {
-			return false, true
+			return updated, !needToUnsetRef
 		}
 		for _, paramStr := range opts.parameters {
 			helmParams := source.Helm.Parameters
@@ -970,9 +1015,10 @@ func unset(source *argoappv1.ApplicationSource, opts unsetOpts) (updated bool, n
 			updated = true
 		}
 	}
+
 	if source.Plugin != nil {
 		if len(opts.pluginEnvs) == 0 {
-			return false, true
+			return false, !needToUnsetRef
 		}
 		for _, env := range opts.pluginEnvs {
 			err := source.Plugin.RemoveEnvEntry(env)
@@ -2419,11 +2465,11 @@ func waitOnApplicationStatus(ctx context.Context, acdClient argocdclient.Client,
 // setParameterOverrides updates an existing or appends a new parameter override in the application
 // the app is assumed to be a helm app and is expected to be in the form:
 // param=value
-func setParameterOverrides(app *argoappv1.Application, parameters []string) {
+func setParameterOverrides(app *argoappv1.Application, parameters []string, index int) {
 	if len(parameters) == 0 {
 		return
 	}
-	source := app.Spec.GetSource()
+	source := app.Spec.GetSourcePtr(index)
 	var sourceType argoappv1.ApplicationSourceType
 	if st, _ := source.ExplicitType(); st != nil {
 		sourceType = *st
@@ -2731,7 +2777,9 @@ func NewApplicationTerminateOpCommand(clientOpts *argocdclient.ClientOptions) *c
 }
 
 func NewApplicationEditCommand(clientOpts *argocdclient.ClientOptions) *cobra.Command {
-	var appNamespace string
+	var (
+		appNamespace string
+	)
 	var command = &cobra.Command{
 		Use:   "edit APPNAME",
 		Short: "Edit application",
@@ -2742,6 +2790,7 @@ func NewApplicationEditCommand(clientOpts *argocdclient.ClientOptions) *cobra.Co
 				c.HelpFunc()(c, args)
 				os.Exit(1)
 			}
+
 			appName, appNs := argo.ParseFromQualifiedName(args[0], appNamespace)
 			conn, appIf := headless.NewClientOrDie(clientOpts, c).NewApplicationClientOrDie()
 			defer argoio.Close(conn)
@@ -2768,7 +2817,11 @@ func NewApplicationEditCommand(clientOpts *argocdclient.ClientOptions) *cobra.Co
 				}
 
 				var appOpts cmdutil.AppOptions
-				cmdutil.SetAppSpecOptions(c.Flags(), &app.Spec, &appOpts)
+
+				// do not allow overrides for applications with multiple sources
+				if !app.Spec.HasMultipleSources() {
+					cmdutil.SetAppSpecOptions(c.Flags(), &app.Spec, &appOpts, 0)
+				}
 				_, err = appIf.UpdateSpec(ctx, &application.ApplicationUpdateSpecRequest{
 					Name:         &appName,
 					Spec:         &updatedSpec,
@@ -2871,8 +2924,12 @@ func NewApplicationAddSourceCommand(clientOpts *argocdclient.ClientOptions) *cob
 			if len(app.Spec.Sources) > 0 {
 				appSource, _ := cmdutil.ConstructSource(&argoappv1.ApplicationSource{}, appOpts, c.Flags())
 
+				// sourceIndex is the index at which new source will be appended to spec.Sources
+				sourceIndex := len(app.Spec.GetSources())
 				app.Spec.Sources = append(app.Spec.Sources, *appSource)
 
+				setParameterOverrides(app, appOpts.Parameters, sourceIndex)
+
 				_, err = appIf.UpdateSpec(ctx, &application.ApplicationUpdateSpecRequest{
 					Name:         &app.Name,
 					Spec:         &app.Spec,
@@ -2895,13 +2952,13 @@ func NewApplicationAddSourceCommand(clientOpts *argocdclient.ClientOptions) *cob
 // NewApplicationRemoveSourceCommand returns a new instance of an `argocd app remove-source` command
 func NewApplicationRemoveSourceCommand(clientOpts *argocdclient.ClientOptions) *cobra.Command {
 	var (
-		source_index int
+		sourceIndex  int
 		appNamespace string
 	)
 	command := &cobra.Command{
 		Use:   "remove-source APPNAME",
-		Short: "Remove a source from multiple sources application. Index starts with 0.",
-		Example: `  # Remove the source at index 1 from application's sources
+		Short: "Remove a source from multiple sources application. Index starts with 1. Default value is -1.",
+		Example: `  # Remove the source at index 1 from application's sources. Index starts at 1.
   argocd app remove-source myapplication --source-index 1`,
 		Run: func(c *cobra.Command, args []string) {
 			ctx := c.Context()
@@ -2911,8 +2968,8 @@ func NewApplicationRemoveSourceCommand(clientOpts *argocdclient.ClientOptions) *
 				os.Exit(1)
 			}
 
-			if source_index < 0 {
-				errors.CheckError(fmt.Errorf("Index value of source cannot be less than 0"))
+			if sourceIndex <= 0 {
+				errors.CheckError(fmt.Errorf("Index value of source must be greater than 0"))
 			}
 
 			argocdClient := headless.NewClientOrDie(clientOpts, c)
@@ -2936,11 +2993,11 @@ func NewApplicationRemoveSourceCommand(clientOpts *argocdclient.ClientOptions) *
 				errors.CheckError(fmt.Errorf("Cannot remove the only source remaining in the app"))
 			}
 
-			if len(app.Spec.GetSources()) <= source_index {
-				errors.CheckError(fmt.Errorf("Application does not have source at %d\n", source_index))
+			if len(app.Spec.GetSources()) < sourceIndex {
+				errors.CheckError(fmt.Errorf("Application does not have source at %d\n", sourceIndex))
 			}
 
-			app.Spec.Sources = append(app.Spec.Sources[:source_index], app.Spec.Sources[source_index+1:]...)
+			app.Spec.Sources = append(app.Spec.Sources[:sourceIndex-1], app.Spec.Sources[sourceIndex:]...)
 
 			_, err = appIf.UpdateSpec(ctx, &application.ApplicationUpdateSpecRequest{
 				Name:         &app.Name,
@@ -2953,6 +3010,6 @@ func NewApplicationRemoveSourceCommand(clientOpts *argocdclient.ClientOptions) *
 		},
 	}
 	command.Flags().StringVarP(&appNamespace, "app-namespace", "N", "", "Namespace of the target application where the source will be appended")
-	command.Flags().IntVar(&source_index, "source-index", -1, "Index of the source from the list of sources of the app. Index starts from 0.")
+	command.Flags().IntVar(&sourceIndex, "source-index", -1, "Index of the source from the list of sources of the app. Index starts from 1.")
 	return command
 }
diff --git a/cmd/util/app.go b/cmd/util/app.go
index 9a284b56ce38b..b1693689004c4 100644
--- a/cmd/util/app.go
+++ b/cmd/util/app.go
@@ -139,16 +139,27 @@ func AddAppFlags(command *cobra.Command, opts *AppOptions) {
 	command.Flags().StringVar(&opts.ref, "ref", "", "Ref is reference to another source within sources field")
 }
 
-func SetAppSpecOptions(flags *pflag.FlagSet, spec *argoappv1.ApplicationSpec, appOpts *AppOptions) int {
+func SetAppSpecOptions(flags *pflag.FlagSet, spec *argoappv1.ApplicationSpec, appOpts *AppOptions, index int) int {
 	visited := 0
 	if flags == nil {
 		return visited
 	}
-	source := spec.GetSourcePtr()
+	source := spec.GetSourcePtr(index)
 	if source == nil {
 		source = &argoappv1.ApplicationSource{}
 	}
 	source, visited = ConstructSource(source, *appOpts, flags)
+	if spec.HasMultipleSources() {
+		if index == 0 {
+			spec.Sources[index] = *source
+		} else if index > 0 {
+			spec.Sources[index-1] = *source
+		} else {
+			spec.Sources = append(spec.Sources, *source)
+		}
+	} else {
+		spec.Source = source
+	}
 	flags.Visit(func(f *pflag.Flag) {
 		visited++
 
@@ -220,7 +231,6 @@ func SetAppSpecOptions(flags *pflag.FlagSet, spec *argoappv1.ApplicationSpec, ap
 				log.Fatalf("Invalid sync-retry-limit [%d]", appOpts.retryLimit)
 			}
 		}
-		spec.Source = source
 	})
 	if flags.Changed("auto-prune") {
 		if spec.SyncPolicy == nil || spec.SyncPolicy.Automated == nil {
@@ -414,11 +424,11 @@ func setJsonnetOptLibs(src *argoappv1.ApplicationSource, libs []string) {
 // SetParameterOverrides updates an existing or appends a new parameter override in the application
 // The app is assumed to be a helm app and is expected to be in the form:
 // param=value
-func SetParameterOverrides(app *argoappv1.Application, parameters []string) {
+func SetParameterOverrides(app *argoappv1.Application, parameters []string, index int) {
 	if len(parameters) == 0 {
 		return
 	}
-	source := app.Spec.GetSource()
+	source := app.Spec.GetSourcePtr(index)
 	var sourceType argoappv1.ApplicationSourceType
 	if st, _ := source.ExplicitType(); st != nil {
 		sourceType = *st
@@ -530,8 +540,8 @@ func constructAppsBaseOnName(appName string, labels, annotations, args []string,
 			Source: &argoappv1.ApplicationSource{},
 		},
 	}
-	SetAppSpecOptions(flags, &app.Spec, &appOpts)
-	SetParameterOverrides(app, appOpts.Parameters)
+	SetAppSpecOptions(flags, &app.Spec, &appOpts, 0)
+	SetParameterOverrides(app, appOpts.Parameters, 0)
 	mergeLabels(app, labels)
 	setAnnotations(app, annotations)
 	return []*argoappv1.Application{
@@ -557,10 +567,14 @@ func constructAppsFromFileUrl(fileURL, appName string, labels, annotations, args
 			return nil, fmt.Errorf("app.Name is empty. --name argument can be used to provide app.Name")
 		}
 
-		SetAppSpecOptions(flags, &app.Spec, &appOpts)
-		SetParameterOverrides(app, appOpts.Parameters)
 		mergeLabels(app, labels)
 		setAnnotations(app, annotations)
+
+		// do not allow overrides for applications with multiple sources
+		if !app.Spec.HasMultipleSources() {
+			SetAppSpecOptions(flags, &app.Spec, &appOpts, 0)
+			SetParameterOverrides(app, appOpts.Parameters, 0)
+		}
 	}
 	return apps, nil
 }
diff --git a/cmd/util/app_test.go b/cmd/util/app_test.go
index b5fce9c1e663e..5e95eeb388634 100644
--- a/cmd/util/app_test.go
+++ b/cmd/util/app_test.go
@@ -170,7 +170,16 @@ func (f *appOptionsFixture) SetFlag(key, value string) error {
 	if err != nil {
 		return err
 	}
-	_ = SetAppSpecOptions(f.command.Flags(), f.spec, f.options)
+	_ = SetAppSpecOptions(f.command.Flags(), f.spec, f.options, 0)
+	return err
+}
+
+func (f *appOptionsFixture) SetFlagWithSourceIndex(key, value string, index int) error {
+	err := f.command.Flags().Set(key, value)
+	if err != nil {
+		return err
+	}
+	_ = SetAppSpecOptions(f.command.Flags(), f.spec, f.options, index)
 	return err
 }
 
@@ -225,6 +234,54 @@ func Test_setAppSpecOptions(t *testing.T) {
 	})
 }
 
+func newMultiSourceAppOptionsFixture() *appOptionsFixture {
+	fixture := &appOptionsFixture{
+		spec: &v1alpha1.ApplicationSpec{
+			Sources: v1alpha1.ApplicationSources{
+				v1alpha1.ApplicationSource{},
+				v1alpha1.ApplicationSource{},
+			},
+		},
+		command: &cobra.Command{},
+		options: &AppOptions{},
+	}
+	AddAppFlags(fixture.command, fixture.options)
+	return fixture
+}
+
+func Test_setAppSpecOptionsMultiSourceApp(t *testing.T) {
+	f := newMultiSourceAppOptionsFixture()
+	index := 0
+	index1 := 1
+	index2 := 2
+	t.Run("SyncPolicy", func(t *testing.T) {
+		assert.NoError(t, f.SetFlagWithSourceIndex("sync-policy", "automated", index1))
+		assert.NotNil(t, f.spec.SyncPolicy.Automated)
+
+		f.spec.SyncPolicy = nil
+		assert.NoError(t, f.SetFlagWithSourceIndex("sync-policy", "automatic", index1))
+		assert.NotNil(t, f.spec.SyncPolicy.Automated)
+	})
+	t.Run("Helm - Index 0", func(t *testing.T) {
+		assert.NoError(t, f.SetFlagWithSourceIndex("helm-version", "v2", index))
+		assert.Equal(t, len(f.spec.GetSources()), 2)
+		assert.Equal(t, f.spec.GetSources()[index].Helm.Version, "v2")
+	})
+	t.Run("Kustomize", func(t *testing.T) {
+		assert.NoError(t, f.SetFlagWithSourceIndex("kustomize-replica", "my-deployment=2", index1))
+		assert.Equal(t, f.spec.Sources[index1-1].Kustomize.Replicas, v1alpha1.KustomizeReplicas{{Name: "my-deployment", Count: intstr.FromInt(2)}})
+		assert.NoError(t, f.SetFlagWithSourceIndex("kustomize-replica", "my-deployment=4", index2))
+		assert.Equal(t, f.spec.Sources[index2-1].Kustomize.Replicas, v1alpha1.KustomizeReplicas{{Name: "my-deployment", Count: intstr.FromInt(4)}})
+	})
+	t.Run("Helm", func(t *testing.T) {
+		assert.NoError(t, f.SetFlagWithSourceIndex("helm-version", "v2", index1))
+		assert.NoError(t, f.SetFlagWithSourceIndex("helm-version", "v3", index2))
+		assert.Equal(t, len(f.spec.GetSources()), 2)
+		assert.Equal(t, f.spec.GetSources()[index1-1].Helm.Version, "v2")
+		assert.Equal(t, f.spec.GetSources()[index2-1].Helm.Version, "v3")
+	})
+}
+
 func Test_setAnnotations(t *testing.T) {
 	t.Run("Annotations", func(t *testing.T) {
 		app := v1alpha1.Application{}
diff --git a/docs/user-guide/commands/argocd_app.md b/docs/user-guide/commands/argocd_app.md
index ff8fe0d4a01b6..a5878502ce5c7 100644
--- a/docs/user-guide/commands/argocd_app.md
+++ b/docs/user-guide/commands/argocd_app.md
@@ -91,7 +91,7 @@ argocd app [flags]
 * [argocd app manifests](argocd_app_manifests.md)	 - Print manifests of an application
 * [argocd app patch](argocd_app_patch.md)	 - Patch application
 * [argocd app patch-resource](argocd_app_patch-resource.md)	 - Patch resource in an application
-* [argocd app remove-source](argocd_app_remove-source.md)	 - Remove a source from multiple sources application. Index starts with 0.
+* [argocd app remove-source](argocd_app_remove-source.md)	 - Remove a source from multiple sources application. Index starts with 1. Default value is -1.
 * [argocd app resources](argocd_app_resources.md)	 - List resource of application
 * [argocd app rollback](argocd_app_rollback.md)	 - Rollback application to a previous deployed version by History ID, omitted will Rollback to the previous version
 * [argocd app set](argocd_app_set.md)	 - Set application parameters
diff --git a/docs/user-guide/commands/argocd_app_create.md b/docs/user-guide/commands/argocd_app_create.md
index 00b4949f7993b..fb147b8e4aa9f 100644
--- a/docs/user-guide/commands/argocd_app_create.md
+++ b/docs/user-guide/commands/argocd_app_create.md
@@ -26,6 +26,9 @@ argocd app create APPNAME [flags]
   # Create a Kustomize app
   argocd app create kustomize-guestbook --repo https://github.com/argoproj/argocd-example-apps.git --path kustomize-guestbook --dest-namespace default --dest-server https://kubernetes.default.svc --kustomize-image gcr.io/heptio-images/ks-guestbook-demo:0.1
 
+  # Create a MultiSource app while yaml file contains an application with multiple sources
+  argocd app create guestbook --file <path-to-yaml-file>
+
   # Create a app using a custom tool:
   argocd app create kasane --repo https://github.com/argoproj/argocd-example-apps.git --path plugins/kasane --dest-namespace default --dest-server https://kubernetes.default.svc --config-management-plugin kasane
 ```
diff --git a/docs/user-guide/commands/argocd_app_remove-source.md b/docs/user-guide/commands/argocd_app_remove-source.md
index b7bd0df09823d..b9f29d8c6eb45 100644
--- a/docs/user-guide/commands/argocd_app_remove-source.md
+++ b/docs/user-guide/commands/argocd_app_remove-source.md
@@ -2,7 +2,7 @@
 
 ## argocd app remove-source
 
-Remove a source from multiple sources application. Index starts with 0.
+Remove a source from multiple sources application. Index starts with 1. Default value is -1.
 
 ```
 argocd app remove-source APPNAME [flags]
@@ -11,7 +11,7 @@ argocd app remove-source APPNAME [flags]
 ### Examples
 
 ```
-  # Remove the source at index 1 from application's sources
+  # Remove the source at index 1 from application's sources. Index starts at 1.
   argocd app remove-source myapplication --source-index 1
 ```
 
@@ -20,7 +20,7 @@ argocd app remove-source APPNAME [flags]
 ```
   -N, --app-namespace string   Namespace of the target application where the source will be appended
   -h, --help                   help for remove-source
-      --source-index int       Index of the source from the list of sources of the app. Index starts from 0. (default -1)
+      --source-index int       Index of the source from the list of sources of the app. Index starts from 1. (default -1)
 ```
 
 ### Options inherited from parent commands
diff --git a/docs/user-guide/commands/argocd_app_set.md b/docs/user-guide/commands/argocd_app_set.md
index 1c6cc40bd5c27..97288ad775345 100644
--- a/docs/user-guide/commands/argocd_app_set.md
+++ b/docs/user-guide/commands/argocd_app_set.md
@@ -23,6 +23,9 @@ argocd app set APPNAME [flags]
   # Set and override application parameters with a parameter file
   argocd app set my-app --parameter-file path/to/parameter-file.yaml
   
+  # Set and override application parameters for a source at index 1 under spec.sources of app my-app. source-index starts at 1.
+  argocd app set my-app --source-index 1 --repo https://github.com/argoproj/argocd-example-apps.git
+  
   # Set application parameters and specify the namespace
   argocd app set my-app --parameter key1=value1 --parameter key2=value2 --namespace my-namespace
 ```
@@ -76,6 +79,7 @@ argocd app set APPNAME [flags]
       --revision string                            The tracking source branch, tag, commit or Helm chart version the application will sync to
       --revision-history-limit int                 How many items to keep in revision history (default 10)
       --self-heal                                  Set self healing when sync is automated
+      --source-index int                           Index of the source from the list of sources of the app. Index starts at 1. (default -1)
       --sync-option Prune=false                    Add or remove a sync option, e.g add Prune=false. Remove using `!` prefix, e.g. `!Prune=false`
       --sync-policy string                         Set the sync policy (one of: manual (aliases of manual: none), automated (aliases of automated: auto, automatic))
       --sync-retry-backoff-duration duration       Sync retry backoff base duration. Input needs to be a duration (e.g. 2m, 1h) (default 5s)
diff --git a/docs/user-guide/commands/argocd_app_unset.md b/docs/user-guide/commands/argocd_app_unset.md
index 34194b02d447c..0c3bf25d7fa91 100644
--- a/docs/user-guide/commands/argocd_app_unset.md
+++ b/docs/user-guide/commands/argocd_app_unset.md
@@ -14,9 +14,12 @@ argocd app unset APPNAME parameters [flags]
   # Unset kustomize override kustomize image
   argocd app unset my-app --kustomize-image=alpine
 
-  # Unset kustomize override prefix
+  # Unset kustomize override suffix
   argocd app unset my-app --namesuffix
 
+  # Unset kustomize override suffix for source at index 1 under spec.sources of app my-app. source-index starts at 1.
+  argocd app unset my-app --source-index 1 --namesuffix
+
   # Unset parameter override
   argocd app unset my-app -p COMPONENT=PARAM
 ```
@@ -36,6 +39,8 @@ argocd app unset APPNAME parameters [flags]
   -p, --parameter stringArray           Unset a parameter override (e.g. -p guestbook=image)
       --pass-credentials                Unset passCredentials
       --plugin-env stringArray          Unset plugin env variables (e.g --plugin-env name)
+      --ref                             Unset ref on the source
+      --source-index int                Index of the source from the list of sources of the app. Index starts at 1. (default -1)
       --values stringArray              Unset one or more Helm values files
       --values-literal                  Unset literal Helm values block
 ```
diff --git a/pkg/apis/application/v1alpha1/types.go b/pkg/apis/application/v1alpha1/types.go
index fc2908c4643dc..abd2735710e72 100644
--- a/pkg/apis/application/v1alpha1/types.go
+++ b/pkg/apis/application/v1alpha1/types.go
@@ -230,9 +230,12 @@ func (a *ApplicationSpec) HasMultipleSources() bool {
 	return a.Sources != nil && len(a.Sources) > 0
 }
 
-func (a *ApplicationSpec) GetSourcePtr() *ApplicationSource {
+func (a *ApplicationSpec) GetSourcePtr(index int) *ApplicationSource {
 	// if Application has multiple sources, return the first source in sources
 	if a.HasMultipleSources() {
+		if index > 0 {
+			return &a.Sources[index-1]
+		}
 		return &a.Sources[0]
 	}
 	return a.Source
diff --git a/server/repository/repository_test.go b/server/repository/repository_test.go
index 9c294b5a332b9..55bf7ab7220ac 100644
--- a/server/repository/repository_test.go
+++ b/server/repository/repository_test.go
@@ -654,7 +654,7 @@ func TestRepositoryServerGetAppDetails(t *testing.T) {
 
 		s := NewServer(&repoServerClientset, db, enforcer, newFixtures().Cache, appLister, projLister, testNamespace, settingsMgr)
 		resp, err := s.GetAppDetails(context.TODO(), &repository.RepoAppDetailsQuery{
-			Source:     guestbookApp.Spec.GetSourcePtr(),
+			Source:     guestbookApp.Spec.GetSourcePtr(0),
 			AppName:    "guestbook",
 			AppProject: "default",
 		})
@@ -752,7 +752,7 @@ func TestRepositoryServerGetAppDetails(t *testing.T) {
 
 		s := NewServer(&repoServerClientset, db, enforcer, newFixtures().Cache, appLister, projLister, testNamespace, settingsMgr)
 		resp, err := s.GetAppDetails(context.TODO(), &repository.RepoAppDetailsQuery{
-			Source:     guestbookApp.Spec.GetSourcePtr(),
+			Source:     guestbookApp.Spec.GetSourcePtr(0),
 			AppName:    "guestbook",
 			AppProject: "mismatch",
 		})
diff --git a/util/notification/expression/repo/repo.go b/util/notification/expression/repo/repo.go
index a782c0b7c1725..8456774f0869a 100644
--- a/util/notification/expression/repo/repo.go
+++ b/util/notification/expression/repo/repo.go
@@ -33,7 +33,7 @@ func getApplicationSourceAndName(obj *unstructured.Unstructured) (*v1alpha1.Appl
 	if err != nil {
 		return nil, "", err
 	}
-	return application.Spec.GetSourcePtr(), application.GetName(), nil
+	return application.Spec.GetSourcePtr(0), application.GetName(), nil
 }
 
 func getAppDetails(app *unstructured.Unstructured, argocdService service.Service) (*shared.AppDetail, error) {