diff --git a/pkg/agent/flannel/setup.go b/pkg/agent/flannel/setup.go
index fc21b51d52..a1f290897d 100644
--- a/pkg/agent/flannel/setup.go
+++ b/pkg/agent/flannel/setup.go
@@ -81,7 +81,8 @@ const (
 
 	wireguardNativeBackend = `{
 	"Type": "wireguard",
-	"PersistentKeepaliveInterval": 25
+	"PersistentKeepaliveInterval": %PersistentKeepaliveInterval%,
+	"Mode": "%Mode%"
 }`
 
 	emptyIPv6Network = "::/0"
@@ -206,8 +207,22 @@ func createFlannelConf(nodeConfig *config.Node) error {
 	}
 
 	var backendConf string
+	parts := strings.SplitN(nodeConfig.FlannelBackend, "=", 2)
+	backend := parts[0]
+	backendOptions := make(map[string]string)
+	if len(parts) > 1 {
+		options := strings.Split(parts[1], ",")
+		for _, o := range options {
+			p := strings.SplitN(o, "=", 2)
+			if len(p) == 1 {
+				backendOptions[p[0]] = ""
+			} else {
+				backendOptions[p[0]] = p[1]
+			}
+		}
+	}
 
-	switch nodeConfig.FlannelBackend {
+	switch backend {
 	case config.FlannelBackendVXLAN:
 		backendConf = vxlanBackend
 	case config.FlannelBackendHostGW:
@@ -221,7 +236,16 @@ func createFlannelConf(nodeConfig *config.Node) error {
 		backendConf = strings.ReplaceAll(wireguardBackend, "%flannelConfDir%", filepath.Dir(nodeConfig.FlannelConfFile))
 		logrus.Warnf("The wireguard backend is deprecated and will be removed in k3s v1.26, please switch to wireguard-native. Check our docs for information about how to migrate")
 	case config.FlannelBackendWireguardNative:
-		backendConf = wireguardNativeBackend
+		mode, ok := backendOptions["Mode"]
+		if !ok {
+			mode = "separate"
+		}
+		keepalive, ok := backendOptions["PersistentKeepaliveInterval"]
+		if !ok {
+			keepalive = "25"
+		}
+		backendConf = strings.ReplaceAll(wireguardNativeBackend, "%Mode%", mode)
+		backendConf = strings.ReplaceAll(backendConf, "%PersistentKeepaliveInterval%", keepalive)
 	default:
 		return fmt.Errorf("Cannot configure unknown flannel backend '%s'", nodeConfig.FlannelBackend)
 	}
diff --git a/pkg/cli/cmds/server.go b/pkg/cli/cmds/server.go
index cc03ddd46a..04b429feb2 100644
--- a/pkg/cli/cmds/server.go
+++ b/pkg/cli/cmds/server.go
@@ -206,7 +206,7 @@ var ServerFlags = []cli.Flag{
 	ClusterDomain,
 	cli.StringFlag{
 		Name:        "flannel-backend",
-		Usage:       "(networking) One of 'none', 'vxlan', 'ipsec', 'host-gw', 'wireguard'(deprecated), or 'wireguard-native'",
+		Usage:       "(networking) backend<=option1=val1,option2=val2> where backend is one of 'none', 'vxlan', 'ipsec', 'host-gw', 'wireguard-native', or 'wireguard' (deprecated)",
 		Destination: &ServerConfig.FlannelBackend,
 		Value:       "vxlan",
 	},