diff --git a/cli/command/stack/cmd.go b/cli/command/stack/cmd.go
index f4ded77169..8248ad240d 100644
--- a/cli/command/stack/cmd.go
+++ b/cli/command/stack/cmd.go
@@ -69,7 +69,9 @@ func NewStackCommand(dockerCli command.Cli) *cobra.Command {
 	flags := cmd.PersistentFlags()
 	flags.String("kubeconfig", "", "Kubernetes config file")
 	flags.SetAnnotation("kubeconfig", "kubernetes", nil)
+	flags.SetAnnotation("kubeconfig", "deprecated", nil)
 	flags.String("orchestrator", "", "Orchestrator to use (swarm|kubernetes|all)")
+	flags.SetAnnotation("orchestrator", "deprecated", nil)
 	return cmd
 }
 
diff --git a/cli/command/stack/kubernetes/cli.go b/cli/command/stack/kubernetes/cli.go
index a531846809..9b6d50473b 100644
--- a/cli/command/stack/kubernetes/cli.go
+++ b/cli/command/stack/kubernetes/cli.go
@@ -50,6 +50,7 @@ func NewOptions(flags *flag.FlagSet, orchestrator command.Orchestrator) Options
 func AddNamespaceFlag(flags *flag.FlagSet) {
 	flags.String("namespace", "", "Kubernetes namespace to use")
 	flags.SetAnnotation("namespace", "kubernetes", nil)
+	flags.SetAnnotation("namespace", "deprecated", nil)
 }
 
 // WrapCli wraps command.Cli with kubernetes specifics
diff --git a/cli/command/stack/list.go b/cli/command/stack/list.go
index 5175ea371c..412cc2e5ee 100644
--- a/cli/command/stack/list.go
+++ b/cli/command/stack/list.go
@@ -30,8 +30,10 @@ func newListCommand(dockerCli command.Cli, common *commonOptions) *cobra.Command
 	flags.StringVar(&opts.Format, "format", "", "Pretty-print stacks using a Go template")
 	flags.StringSliceVar(&opts.Namespaces, "namespace", []string{}, "Kubernetes namespaces to use")
 	flags.SetAnnotation("namespace", "kubernetes", nil)
+	flags.SetAnnotation("namespace", "deprecated", nil)
 	flags.BoolVarP(&opts.AllNamespaces, "all-namespaces", "", false, "List stacks from all Kubernetes namespaces")
 	flags.SetAnnotation("all-namespaces", "kubernetes", nil)
+	flags.SetAnnotation("all-namespaces", "deprecated", nil)
 	return cmd
 }
 
diff --git a/cli/command/system/version.go b/cli/command/system/version.go
index c086822c88..418ce651c0 100644
--- a/cli/command/system/version.go
+++ b/cli/command/system/version.go
@@ -114,6 +114,7 @@ func NewVersionCommand(dockerCli command.Cli) *cobra.Command {
 	flags.StringVarP(&opts.format, "format", "f", "", "Format the output using the given Go template")
 	flags.StringVar(&opts.kubeConfig, "kubeconfig", "", "Kubernetes config file")
 	flags.SetAnnotation("kubeconfig", "kubernetes", nil)
+	flags.SetAnnotation("kubeconfig", "deprecated", nil)
 
 	return cmd
 }
diff --git a/docs/yaml/yaml.go b/docs/yaml/yaml.go
index 82c90973c0..9ffd8bba3a 100644
--- a/docs/yaml/yaml.go
+++ b/docs/yaml/yaml.go
@@ -199,6 +199,9 @@ func genFlagResult(flags *pflag.FlagSet) []cmdOption {
 		if _, ok := flag.Annotations["experimental"]; ok {
 			opt.Experimental = true
 		}
+		if _, ok := flag.Annotations["deprecated"]; ok {
+			opt.Deprecated = true
+		}
 		if v, ok := flag.Annotations["version"]; ok {
 			opt.MinAPIVersion = v[0]
 		}