diff --git a/pkg/agent/config/config.go b/pkg/agent/config/config.go
index 10d82ba53a..2813de631a 100644
--- a/pkg/agent/config/config.go
+++ b/pkg/agent/config/config.go
@@ -515,8 +515,7 @@ func get(ctx context.Context, envInfo *cmds.Agent, proxy proxy.Proxy) (*config.N
 	if nodeConfig.FlannelBackend == config.FlannelBackendNone {
 		nodeConfig.NoFlannel = true
 	} else if envInfo.NoFlannel {
-		logrus.Warn("no-flannel is deprecated, it will be removed in v1.25. Use --flannel-backend=none instead.")
-		nodeConfig.NoFlannel = envInfo.NoFlannel
+		logrus.Fatal("no-flannel is deprecated. Use --flannel-backend=none instead.")
 	} else {
 		nodeConfig.NoFlannel = envInfo.NoFlannel
 	}
diff --git a/pkg/cli/agent/agent.go b/pkg/cli/agent/agent.go
index 569a95fe9f..aeede9c91a 100644
--- a/pkg/cli/agent/agent.go
+++ b/pkg/cli/agent/agent.go
@@ -46,8 +46,7 @@ func Run(ctx *cli.Context) error {
 	}
 
 	if cmds.AgentConfig.Token == "" && cmds.AgentConfig.ClusterSecret != "" {
-		logrus.Warn("cluster-secret is deprecated, it will be removed in v1.25. Use --token instead.")
-		cmds.AgentConfig.Token = cmds.AgentConfig.ClusterSecret
+		logrus.Fatal("cluster-secret is deprecated. Use --token instead.")
 	}
 
 	if cmds.AgentConfig.Token == "" {
diff --git a/pkg/cli/cmds/server.go b/pkg/cli/cmds/server.go
index 3773267268..bf1d6f22ee 100644
--- a/pkg/cli/cmds/server.go
+++ b/pkg/cli/cmds/server.go
@@ -476,6 +476,12 @@ var ServerFlags = []cli.Flag{
 	PauseImageFlag,
 	SnapshotterFlag,
 	PrivateRegistryFlag,
+	cli.StringFlag{
+		Name:        "system-default-registry",
+		Usage:       "(agent/runtime) Private registry to be used for all system images",
+		EnvVar:      version.ProgramUpper + "_SYSTEM_DEFAULT_REGISTRY",
+		Destination: &ServerConfig.SystemDefaultRegistry,
+	},
 	AirgapExtraRegistryFlag,
 	NodeIPFlag,
 	NodeExternalIPFlag,
@@ -501,12 +507,6 @@ var ServerFlags = []cli.Flag{
 		Usage:       "(experimental) Enable Secret encryption at rest",
 		Destination: &ServerConfig.EncryptSecrets,
 	},
-	cli.StringFlag{
-		Name:        "system-default-registry",
-		Usage:       "(image) Private registry to be used for all system images",
-		EnvVar:      version.ProgramUpper + "_SYSTEM_DEFAULT_REGISTRY",
-		Destination: &ServerConfig.SystemDefaultRegistry,
-	},
 	&SELinuxFlag,
 	LBServerPortFlag,
 
diff --git a/pkg/cli/server/server.go b/pkg/cli/server/server.go
index caaa207092..d1ee245d68 100644
--- a/pkg/cli/server/server.go
+++ b/pkg/cli/server/server.go
@@ -88,8 +88,7 @@ func run(app *cli.Context, cfg *cmds.Server, leaderControllers server.CustomCont
 	}
 
 	if cfg.Token == "" && cfg.ClusterSecret != "" {
-		logrus.Warn("cluster-secret is deprecated, it will be removed in v1.25. Use --token instead.")
-		cfg.Token = cfg.ClusterSecret
+		logrus.Fatal("cluster-secret is deprecated. Use --token instead.")
 	}
 
 	agentReady := make(chan struct{})
@@ -348,12 +347,8 @@ func run(app *cli.Context, cfg *cmds.Server, leaderControllers server.CustomCont
 	}
 
 	serverConfig.ControlConfig.Skips = map[string]bool{}
-	for _, noDeploy := range app.StringSlice("no-deploy") {
-		logrus.Warn("no-deploy flag is deprecated, it will be removed in v1.25. Use --skip-deploy instead.")
-		for _, v := range strings.Split(noDeploy, ",") {
-			v = strings.TrimSpace(v)
-			serverConfig.ControlConfig.Skips[v] = true
-		}
+	if noDeploy := app.StringSlice("no-deploy"); len(noDeploy) > 0 {
+		logrus.Fatal("no-deploy flag is deprecated. Use --skip-deploy instead.")
 	}
 	serverConfig.ControlConfig.Disables = map[string]bool{}
 	for _, disable := range app.StringSlice("disable") {