diff --git a/cmd/run.go b/cmd/run.go
index 6feaf20b..29b06d37 100644
--- a/cmd/run.go
+++ b/cmd/run.go
@@ -20,6 +20,7 @@ import (
 	"os"
 	"path/filepath"
 	"runtime"
+	"slices"
 	"strconv"
 	"strings"
 	"time"
@@ -27,6 +28,7 @@ import (
 	"golang.org/x/mod/semver"
 
 	"github.com/spf13/cobra"
+	"github.com/spf13/pflag"
 	"github.com/spf13/viper"
 
 	daprRuntime "github.com/dapr/dapr/pkg/runtime"
@@ -78,6 +80,15 @@ const (
 	runtimeWaitTimeoutInSeconds = 60
 )
 
+// Flags that are compatible with --run-file
+var runFileCompatibleFlags = []string{
+	"kubernetes",
+	"help",
+	"version",
+	"runtime-path",
+	"log-as-json",
+}
+
 var RunCmd = &cobra.Command{
 	Use:   "run",
 	Short: "Run Dapr and (optionally) your application side by side. Supported platforms: Self-hosted",
@@ -128,6 +139,14 @@ dapr run --run-file /path/to/directory -k
 	},
 	Run: func(cmd *cobra.Command, args []string) {
 		if len(runFilePath) > 0 {
+			// Check for incompatible flags
+			incompatibleFlags := detectIncompatibleFlags(cmd)
+			if len(incompatibleFlags) > 0 {
+				// Print warning message about incompatible flags
+				warningMsg := "The following flags are ignored when using --run-file and should be configured in the run file instead: " + strings.Join(incompatibleFlags, ", ")
+				print.WarningStatusEvent(os.Stdout, warningMsg)
+			}
+
 			runConfigFilePath, err := getRunFilePath(runFilePath)
 			if err != nil {
 				print.FailureStatusEvent(os.Stderr, "Failed to get run file path: %v", err)
@@ -1061,3 +1080,26 @@ func getRunFilePath(path string) (string, error) {
 	}
 	return path, nil
 }
+
+// getConflictingFlags checks if any flags are set other than the ones passed in the excludedFlags slice.
+// Used for logic or notifications when any of the flags are conflicting and should not be used together.
+func getConflictingFlags(cmd *cobra.Command, excludedFlags ...string) []string {
+	var conflictingFlags []string
+	cmd.Flags().Visit(func(f *pflag.Flag) {
+		if !slices.Contains(excludedFlags, f.Name) {
+			conflictingFlags = append(conflictingFlags, f.Name)
+		}
+	})
+	return conflictingFlags
+}
+
+// detectIncompatibleFlags checks if any incompatible flags are used with --run-file
+// and returns a slice of the flag names that were used
+func detectIncompatibleFlags(cmd *cobra.Command) []string {
+	if runFilePath == "" {
+		return nil // No run file specified, so no incompatibilities
+	}
+
+	// Get all flags that are not in the compatible list
+	return getConflictingFlags(cmd, append(runFileCompatibleFlags, "run-file")...)
+}
diff --git a/cmd/run_test.go b/cmd/run_test.go
index 9403a718..5ac0796f 100644
--- a/cmd/run_test.go
+++ b/cmd/run_test.go
@@ -3,6 +3,7 @@ package cmd
 import (
 	"testing"
 
+	"github.com/spf13/cobra"
 	"github.com/stretchr/testify/assert"
 )
 
@@ -17,3 +18,61 @@ func TestValidateSchedulerHostAddress(t *testing.T) {
 		assert.Equal(t, "localhost:50006", address)
 	})
 }
+
+func TestDetectIncompatibleFlags(t *testing.T) {
+	// Setup a temporary run file path to trigger the incompatible flag check
+	originalRunFilePath := runFilePath
+	runFilePath = "some/path"
+	defer func() {
+		// Restore the original runFilePath
+		runFilePath = originalRunFilePath
+	}()
+
+	t.Run("detect incompatible flags", func(t *testing.T) {
+		// Create a test command with flags
+		cmd := &cobra.Command{Use: "test"}
+		cmd.Flags().String("app-id", "", "")
+		cmd.Flags().String("dapr-http-port", "", "")
+		cmd.Flags().String("kubernetes", "", "")   // Compatible flag
+		cmd.Flags().String("runtime-path", "", "") // Compatible flag
+		cmd.Flags().String("log-as-json", "", "")  // Compatible flag
+
+		// Mark flags as changed
+		cmd.Flags().Set("app-id", "myapp")
+		cmd.Flags().Set("dapr-http-port", "3500")
+		cmd.Flags().Set("kubernetes", "true")
+		cmd.Flags().Set("runtime-path", "/path/to/runtime")
+		cmd.Flags().Set("log-as-json", "true")
+
+		// Test detection
+		incompatibleFlags := detectIncompatibleFlags(cmd)
+		assert.Len(t, incompatibleFlags, 2)
+		assert.Contains(t, incompatibleFlags, "app-id")
+		assert.Contains(t, incompatibleFlags, "dapr-http-port")
+		assert.NotContains(t, incompatibleFlags, "kubernetes")
+		assert.NotContains(t, incompatibleFlags, "runtime-path")
+		assert.NotContains(t, incompatibleFlags, "log-as-json")
+	})
+
+	t.Run("no incompatible flags when run file not specified", func(t *testing.T) {
+		// Create a test command with flags
+		cmd := &cobra.Command{Use: "test"}
+		cmd.Flags().String("app-id", "", "")
+		cmd.Flags().String("dapr-http-port", "", "")
+
+		// Mark flags as changed
+		cmd.Flags().Set("app-id", "myapp")
+		cmd.Flags().Set("dapr-http-port", "3500")
+
+		// Temporarily clear runFilePath
+		originalRunFilePath := runFilePath
+		runFilePath = ""
+		defer func() {
+			runFilePath = originalRunFilePath
+		}()
+
+		// Test detection
+		incompatibleFlags := detectIncompatibleFlags(cmd)
+		assert.Nil(t, incompatibleFlags)
+	})
+}
diff --git a/go.mod b/go.mod
index ca2ad965..343f95cc 100644
--- a/go.mod
+++ b/go.mod
@@ -24,6 +24,7 @@ require (
 	github.com/pkg/browser v0.0.0-20240102092130-5ac0b6a4141c
 	github.com/shirou/gopsutil v3.21.11+incompatible
 	github.com/spf13/cobra v1.8.1
+	github.com/spf13/pflag v1.0.5
 	github.com/spf13/viper v1.13.0
 	github.com/stretchr/testify v1.10.0
 	golang.org/x/mod v0.22.0
@@ -186,7 +187,6 @@ require (
 	github.com/spf13/afero v1.8.2 // indirect
 	github.com/spf13/cast v1.7.0 // indirect
 	github.com/spf13/jwalterweatherman v1.1.0 // indirect
-	github.com/spf13/pflag v1.0.5 // indirect
 	github.com/spiffe/go-spiffe/v2 v2.1.7 // indirect
 	github.com/stoewer/go-strcase v1.3.0 // indirect
 	github.com/subosito/gotenv v1.4.1 // indirect