diff --git a/cmd/compose/run.go b/cmd/compose/run.go
index 137c2526b..efc5c831a 100644
--- a/cmd/compose/run.go
+++ b/cmd/compose/run.go
@@ -184,7 +184,12 @@ func runCommand(p *ProjectOptions, dockerCli command.Cli, backend api.Service) *
 			return nil
 		}),
 		RunE: Adapt(func(ctx context.Context, args []string) error {
-			project, _, err := p.ToProject(ctx, dockerCli, []string{options.Service}, cgo.WithResolvedPaths(true), cgo.WithDiscardEnvFile)
+			project, _, err := p.ToProject(ctx, dockerCli, []string{options.Service}, cgo.WithResolvedPaths(true), cgo.WithoutEnvironmentResolution)
+			if err != nil {
+				return err
+			}
+
+			project, err = project.WithServicesEnvironmentResolved(true)
 			if err != nil {
 				return err
 			}
diff --git a/pkg/e2e/env_file_test.go b/pkg/e2e/env_file_test.go
index ed7c84318..ccf02efe9 100644
--- a/pkg/e2e/env_file_test.go
+++ b/pkg/e2e/env_file_test.go
@@ -21,6 +21,7 @@ import (
 	"testing"
 
 	"gotest.tools/v3/assert"
+	"gotest.tools/v3/icmd"
 )
 
 func TestRawEnvFile(t *testing.T) {
@@ -37,3 +38,11 @@ func TestUnusedMissingEnvFile(t *testing.T) {
 
 	c.RunDockerComposeCmd(t, "-f", "./fixtures/env_file/compose.yaml", "up", "-d", "serviceA")
 }
+
+func TestRunEnvFile(t *testing.T) {
+	c := NewParallelCLI(t)
+	defer c.cleanupWithDown(t, "run_dotenv")
+
+	res := c.RunDockerComposeCmd(t, "--project-directory", "./fixtures/env_file", "run", "serviceC", "env")
+	res.Assert(t, icmd.Expected{Out: "FOO=BAR"})
+}
diff --git a/pkg/e2e/fixtures/env_file/compose.yaml b/pkg/e2e/fixtures/env_file/compose.yaml
index 07d5dfeb6..9983f5738 100644
--- a/pkg/e2e/fixtures/env_file/compose.yaml
+++ b/pkg/e2e/fixtures/env_file/compose.yaml
@@ -5,4 +5,10 @@ services:
   serviceB:
     image: nginx:latest
     env_file:
-      - /doesnotexist/.env
\ No newline at end of file
+      - /doesnotexist/.env
+
+  serviceC:
+    profiles: ["test"]
+    image: alpine
+    env_file: test.env
+
diff --git a/pkg/e2e/fixtures/env_file/test.env b/pkg/e2e/fixtures/env_file/test.env
new file mode 100644
index 000000000..15c36f50e
--- /dev/null
+++ b/pkg/e2e/fixtures/env_file/test.env
@@ -0,0 +1 @@
+FOO=BAR
\ No newline at end of file