diff --git a/cmd/compose/run.go b/cmd/compose/run.go
index fd18c94fb02..ff2657f79b5 100644
--- a/cmd/compose/run.go
+++ b/cmd/compose/run.go
@@ -36,28 +36,28 @@ import (
 
 type runOptions struct {
 	*composeOptions
-	Service       string
-	Command       []string
-	environment   []string
-	Detach        bool
-	Remove        bool
-	noTty         bool
-	tty           bool
-	interactive   bool
-	user          string
-	workdir       string
-	entrypoint    string
-	entrypointCmd []string
-	labels        []string
-	volumes       []string
-	publish       []string
-	useAliases    bool
-	servicePorts  bool
-	name          string
-	noDeps        bool
-	ignoreOrphans bool
-	quietPull     bool
-	EnvFiles      []string
+	Service         string
+	Command         []string
+	environment     []string
+	Detach          bool
+	Remove          bool
+	noTty           bool
+	tty             bool
+	interactive     bool
+	user            string
+	workdir         string
+	entrypoint      string
+	entrypointCmd   []string
+	labels          []string
+	volumes         []string
+	publish         []string
+	useAliases      bool
+	servicePorts    bool
+	name            string
+	noDeps          bool
+	ignoreOrphans   bool
+	quietPull       bool
+	ServiceEnvFiles []string
 }
 
 func (opts runOptions) apply(project *types.Project) error {
@@ -157,7 +157,7 @@ func runCommand(p *ProjectOptions, streams api.Streams, backend api.Service) *co
 	flags := cmd.Flags()
 	flags.BoolVarP(&opts.Detach, "detach", "d", false, "Run container in background and print container ID")
 	flags.StringArrayVarP(&opts.environment, "env", "e", []string{}, "Set environment variables")
-	flags.StringArrayVar(&opts.EnvFiles, "env-file", []string{}, "Read in a file of environment variables")
+	flags.StringArrayVar(&opts.ServiceEnvFiles, "service-env-file", []string{}, "Read in a file of environment variables")
 	flags.StringArrayVarP(&opts.labels, "label", "l", []string{}, "Add or override a label")
 	flags.BoolVar(&opts.Remove, "rm", false, "Automatically remove the container when it exits")
 	flags.BoolVarP(&opts.noTty, "no-TTY", "T", !streams.Out().IsTerminal(), "Disable pseudo-TTY allocation (default: auto-detected).")
@@ -235,7 +235,7 @@ func runRun(ctx context.Context, backend api.Service, project *types.Project, op
 		NoDeps:            opts.noDeps,
 		Index:             0,
 		QuietPull:         opts.quietPull,
-		EnvFiles:          opts.EnvFiles,
+		ServiceEnvFiles:   opts.ServiceEnvFiles,
 	}
 
 	for i, service := range project.Services {
diff --git a/pkg/api/api.go b/pkg/api/api.go
index fcc36aab424..5820b8ca756 100644
--- a/pkg/api/api.go
+++ b/pkg/api/api.go
@@ -259,8 +259,8 @@ type RunOptions struct {
 	// QuietPull makes the pulling process quiet
 	QuietPull bool
 	// used by exec
-	Index    int
-	EnvFiles []string
+	Index           int
+	ServiceEnvFiles []string
 }
 
 // EventsOptions group options of the Events API
diff --git a/pkg/compose/run.go b/pkg/compose/run.go
index 7bb96e269f9..28ecb5490ab 100644
--- a/pkg/compose/run.go
+++ b/pkg/compose/run.go
@@ -128,7 +128,7 @@ func applyRunOptions(project *types.Project, service *types.ServiceConfig, opts
 		service.Labels = service.Labels.Add(k, v)
 	}
 
-	if opts.EnvFiles != nil {
-		service.EnvFile = opts.EnvFiles
+	if opts.ServiceEnvFiles != nil {
+		service.EnvFile = append(service.EnvFile, opts.ServiceEnvFiles...)
 	}
 }
diff --git a/pkg/compose/run_test.go b/pkg/compose/run_test.go
new file mode 100644
index 00000000000..4cb6f785ee7
--- /dev/null
+++ b/pkg/compose/run_test.go
@@ -0,0 +1,58 @@
+package compose
+
+import (
+	"testing"
+
+	"github.com/compose-spec/compose-go/types"
+	"github.com/docker/compose/v2/pkg/api"
+	"gotest.tools/v3/assert"
+)
+
+func TestServiceEnvFiles(t *testing.T) {
+
+	t.Run("Verify service.EnvFile shouldn't modify", func(t *testing.T) {
+		fooService := types.ServiceConfig{
+			Name:    "foo",
+			EnvFile: []string{},
+		}
+
+		project := types.Project{
+			Name: "test-project",
+			Services: types.Services{
+				fooService,
+			},
+		}
+
+		opts := api.RunOptions{
+			ServiceEnvFiles: nil,
+		}
+
+		applyRunOptions(&project, &fooService, opts)
+
+		assert.Assert(t, len(fooService.EnvFile) == 0)
+	})
+
+	t.Run("Verify appends ServiceEnvFiles", func(t *testing.T) {
+		fooService := &types.ServiceConfig{
+			Name:    "foo",
+			EnvFile: []string{"./existing.env"},
+		}
+
+		project := types.Project{
+			Name: "test-project",
+			Services: types.Services{
+				*fooService,
+			},
+		}
+
+		opts := api.RunOptions{
+			ServiceEnvFiles: []string{"./file.env"},
+		}
+
+		applyRunOptions(&project, fooService, opts)
+
+		assert.Assert(t, len(fooService.EnvFile) == 2)
+		assert.Assert(t, fooService.EnvFile[0] == "./existing.env")
+		assert.Assert(t, fooService.EnvFile[1] == "./file.env")
+	})
+}