diff --git a/cmd/epp/runner/runner.go b/cmd/epp/runner/runner.go
index 2f5c1e388..5a66532f6 100644
--- a/cmd/epp/runner/runner.go
+++ b/cmd/epp/runner/runner.go
@@ -132,8 +132,9 @@ var (
 	configFile = flag.String("config-file", runserver.DefaultConfigFile, "The path to the configuration file")
 	configText = flag.String("config-text", runserver.DefaultConfigText, "The configuration specified as text, in lieu of a file")
 
-	modelServerMetricsPort = flag.Int("model-server-metrics-port", 0, "Port to scrape metrics from pods. "+
-		"Default value will be set to the InferencePool.Spec.TargetPorts[0].Number if not set.")
+	modelServerMetricsPort = flag.Int("model-server-metrics-port", 0, "[DEPRECATED] Port to scrape metrics from pods. "+
+		"Default value will be set to the InferencePool.Spec.TargetPorts[0].Number if not set."+
+		"[DEPRECATED] This option will be removed in the next release.")
 	modelServerMetricsPath                    = flag.String("model-server-metrics-path", "/metrics", "Path to scrape metrics from pods")
 	modelServerMetricsScheme                  = flag.String("model-server-metrics-scheme", "http", "Scheme to scrape metrics from pods")
 	modelServerMetricsHttpsInsecureSkipVerify = flag.Bool("model-server-metrics-https-insecure-skip-verify", true, "When using 'https' scheme for 'model-server-metrics-scheme', configure 'InsecureSkipVerify' (default to true)")
@@ -191,6 +192,8 @@ func (r *Runner) Run(ctx context.Context) error {
 	flag.Parse()
 	initLogging(&opts)
 
+	_ = r.deprecatedFlagsHandler(setupLog) // ignore error for now
+
 	if *tracing {
 		err := common.InitTracing(ctx, setupLog)
 		if err != nil {
@@ -467,6 +470,33 @@ func (r *Runner) parseConfigurationPhaseTwo(ctx context.Context, rawConfig *conf
 	return cfg, nil
 }
 
+func (r *Runner) deprecatedFlagsHandler(logger logr.Logger) error {
+	deprecated := map[string]string{ // Map of deprecated flags: key = flag name, value = replacement (empty if none)
+		"model-server-metrics-port": "",
+	}
+
+	var usedDeprecated []string // Track which deprecated flags were explicitly set
+	flag.Visit(func(f *flag.Flag) {
+		if _, ok := deprecated[f.Name]; ok {
+			usedDeprecated = append(usedDeprecated, f.Name)
+		}
+	})
+
+	if len(usedDeprecated) > 0 { // report on deprecated flags used
+		for _, option := range usedDeprecated {
+			if replacement := deprecated[option]; replacement != "" {
+				logger.Info("deprecated option will be removed in the next release",
+					"option", option, "replacement", replacement)
+			} else {
+				logger.Info("deprecated option will be removed in the next release. No replacement available.",
+					"option", option)
+			}
+		}
+		return errors.New("deprecated options used" + fmt.Sprintf("%+v", usedDeprecated))
+	}
+	return nil
+}
+
 func (r *Runner) deprecatedConfigurationHelper(cfg *config.Config, logger logr.Logger) {
 	// Handle deprecated environment variable based feature flags
 
diff --git a/pkg/epp/datastore/datastore.go b/pkg/epp/datastore/datastore.go
index 5d6ff751b..80d893681 100644
--- a/pkg/epp/datastore/datastore.go
+++ b/pkg/epp/datastore/datastore.go
@@ -69,6 +69,8 @@ type Datastore interface {
 	Clear()
 }
 
+// NewDatastore creates a new data store.
+// TODO: modelServerMetricsPort is being deprecated
 func NewDatastore(parentCtx context.Context, epFactory datalayer.EndpointFactory, modelServerMetricsPort int32) Datastore {
 	store := &datastore{
 		parentCtx:              parentCtx,
@@ -93,7 +95,7 @@ type datastore struct {
 	pods *sync.Map
 	// modelServerMetricsPort metrics port from EPP command line argument
 	// used only if there is only one inference engine per pod
-	modelServerMetricsPort int32
+	modelServerMetricsPort int32 // TODO: deprecating
 	epf                    datalayer.EndpointFactory
 }