diff --git a/cmd/ctr/commands/run/run_unix.go b/cmd/ctr/commands/run/run_unix.go
index 664054f3d..6838d20ad 100644
--- a/cmd/ctr/commands/run/run_unix.go
+++ b/cmd/ctr/commands/run/run_unix.go
@@ -239,10 +239,6 @@ func NewContainer(ctx gocontext.Context, client *containerd.Client, context *cli
 			opts = append(opts, oci.WithAnnotations(annos))
 		}
 
-		if context.Bool("cni") {
-			cniMeta := &commands.NetworkMetaData{EnableCni: true}
-			cOpts = append(cOpts, containerd.WithContainerExtension(commands.CtrCniMetadataExtension, cniMeta))
-		}
 		if caps := context.StringSlice("cap-add"); len(caps) > 0 {
 			for _, cap := range caps {
 				if !strings.HasPrefix(cap, "CAP_") {
@@ -375,6 +371,11 @@ func NewContainer(ctx gocontext.Context, client *containerd.Client, context *cli
 		}
 	}
 
+	if context.Bool("cni") {
+		cniMeta := &commands.NetworkMetaData{EnableCni: true}
+		cOpts = append(cOpts, containerd.WithContainerExtension(commands.CtrCniMetadataExtension, cniMeta))
+	}
+
 	runtimeOpts, err := getRuntimeOptions(context)
 	if err != nil {
 		return nil, err
diff --git a/cmd/ctr/commands/run/run_windows.go b/cmd/ctr/commands/run/run_windows.go
index d22bb2ead..4911346ac 100644
--- a/cmd/ctr/commands/run/run_windows.go
+++ b/cmd/ctr/commands/run/run_windows.go
@@ -131,8 +131,6 @@ func NewContainer(ctx gocontext.Context, client *containerd.Client, context *cli
 				return nil, err
 			}
 			opts = append(opts, oci.WithWindowsNetworkNamespace(ns.GetPath()))
-			cniMeta := &commands.NetworkMetaData{EnableCni: true}
-			cOpts = append(cOpts, containerd.WithContainerExtension(commands.CtrCniMetadataExtension, cniMeta))
 		}
 		if context.Bool("isolated") {
 			opts = append(opts, oci.WithWindowsHyperV)
@@ -165,6 +163,11 @@ func NewContainer(ctx gocontext.Context, client *containerd.Client, context *cli
 		}
 	}
 
+	if context.Bool("cni") {
+		cniMeta := &commands.NetworkMetaData{EnableCni: true}
+		cOpts = append(cOpts, containerd.WithContainerExtension(commands.CtrCniMetadataExtension, cniMeta))
+	}
+
 	runtime := context.String("runtime")
 	var runtimeOpts interface{}
 	if runtime == "io.containerd.runhcs.v1" {