diff --git a/api/exec/compose_stack.go b/api/exec/compose_stack.go
index 3a2776031..9ae3bacd2 100644
--- a/api/exec/compose_stack.go
+++ b/api/exec/compose_stack.go
@@ -76,15 +76,9 @@ func (manager *ComposeStackManager) Down(ctx context.Context, stack *portainer.S
 		defer proxy.Close()
 	}
 
-	envFilePath, err := createEnvFile(stack)
-	if err != nil {
-		return errors.Wrap(err, "failed to create env file")
-	}
-
 	err = manager.deployer.Remove(ctx, stack.Name, nil, libstack.Options{
-		WorkingDir:  stack.ProjectPath,
-		EnvFilePath: envFilePath,
-		Host:        url,
+		WorkingDir: "",
+		Host:       url,
 	})
 
 	return errors.Wrap(err, "failed to remove a stack")
@@ -148,28 +142,46 @@ func createEnvFile(stack *portainer.Stack) (string, error) {
 	}
 	defer envfile.Close()
 
-	copyDefaultEnvFile(stack, envfile)
+	// Copy from default .env file
+	defaultEnvPath := path.Join(stack.ProjectPath, path.Dir(stack.EntryPoint), ".env")
+	if err = copyDefaultEnvFile(envfile, defaultEnvPath); err != nil {
+		return "", err
+	}
 
-	for _, v := range stack.Env {
-		envfile.WriteString(fmt.Sprintf("%s=%s\n", v.Name, v.Value))
+	// Copy from stack env vars
+	if err = copyConfigEnvVars(envfile, stack.Env); err != nil {
+		return "", err
 	}
 
 	return "stack.env", nil
 }
 
 // copyDefaultEnvFile copies the default .env file if it exists to the provided writer
-func copyDefaultEnvFile(stack *portainer.Stack, w io.Writer) {
-	defaultEnvFile, err := os.Open(path.Join(path.Join(stack.ProjectPath, path.Dir(stack.EntryPoint)), ".env"))
+func copyDefaultEnvFile(w io.Writer, defaultEnvFilePath string) error {
+	defaultEnvFile, err := os.Open(defaultEnvFilePath)
 	if err != nil {
 		// If cannot open a default file, then don't need to copy it.
 		// We could as well stat it and check if it exists, but this is more efficient.
-		return
+		return nil
 	}
 
 	defer defaultEnvFile.Close()
 
 	if _, err = io.Copy(w, defaultEnvFile); err == nil {
-		io.WriteString(w, "\n")
+		if _, err = fmt.Fprintf(w, "\n"); err != nil {
+			return fmt.Errorf("failed to copy default env file: %w", err)
+		}
 	}
+	return nil
 	// If couldn't copy the .env file, then ignore the error and try to continue
 }
+
+// copyConfigEnvVars write the environment variables from stack configuration to the writer
+func copyConfigEnvVars(w io.Writer, envs []portainer.Pair) error {
+	for _, v := range envs {
+		if _, err := fmt.Fprintf(w, "%s=%s\n", v.Name, v.Value); err != nil {
+			return fmt.Errorf("failed to copy config env vars: %w", err)
+		}
+	}
+	return nil
+}
diff --git a/api/exec/compose_stack_test.go b/api/exec/compose_stack_test.go
index b1904438a..ddaba66bb 100644
--- a/api/exec/compose_stack_test.go
+++ b/api/exec/compose_stack_test.go
@@ -23,6 +23,7 @@ func Test_createEnvFile(t *testing.T) {
 			name: "should not add env file option if stack doesn't have env variables",
 			stack: &portainer.Stack{
 				ProjectPath: dir,
+				Env:         nil,
 			},
 			expected: "",
 		},
diff --git a/api/exec/swarm_stack.go b/api/exec/swarm_stack.go
index 36d99d2b9..be82af386 100644
--- a/api/exec/swarm_stack.go
+++ b/api/exec/swarm_stack.go
@@ -157,7 +157,10 @@ func runCommandAndCaptureStdErr(command string, args []string, env []string, wor
 	var stderr bytes.Buffer
 	cmd := exec.Command(command, args...)
 	cmd.Stderr = &stderr
-	cmd.Dir = workingDir
+
+	if workingDir != "" {
+		cmd.Dir = workingDir
+	}
 
 	if env != nil {
 		cmd.Env = os.Environ()
diff --git a/api/http/handler/stacks/stack_delete.go b/api/http/handler/stacks/stack_delete.go
index ee63f4de7..a70d46cdf 100644
--- a/api/http/handler/stacks/stack_delete.go
+++ b/api/http/handler/stacks/stack_delete.go
@@ -245,7 +245,16 @@ func (handler *Handler) deleteStack(userID portainer.UserID, stack *portainer.St
 		}
 
 		out, err := handler.KubernetesDeployer.Remove(userID, endpoint, manifestFiles, stack.Namespace)
-
+		if err != nil {
+			for _, manifest := range manifestFiles {
+				if exists, fileExistsErr := filesystem.FileExists(manifest); fileExistsErr != nil || !exists {
+					// If removal has failed and one of the manifest files is missing,
+					// we can consider this stack as removed
+					log.Warn().Err(fileExistsErr).Msgf("failed to find manifest %s, but stack deletion will continue", manifest)
+					return nil
+				}
+			}
+		}
 		return errors.WithMessagef(err, "failed to remove kubernetes resources: %q", out)
 	}
 
diff --git a/pkg/libstack/compose/internal/composeplugin/composeplugin.go b/pkg/libstack/compose/internal/composeplugin/composeplugin.go
index 26d09d4a8..5516da640 100644
--- a/pkg/libstack/compose/internal/composeplugin/composeplugin.go
+++ b/pkg/libstack/compose/internal/composeplugin/composeplugin.go
@@ -136,7 +136,12 @@ func (wrapper *PluginWrapper) command(command composeCommand, options libstack.O
 	args = append(args, command.ToArgs()...)
 
 	cmd := exec.Command(program, args...)
-	cmd.Dir = options.WorkingDir
+	if options.WorkingDir != "" {
+		// Specify an non-exist working directory will cause the failure
+		// of the "docker-compose down" command even if the project name
+		// is correct.
+		cmd.Dir = options.WorkingDir
+	}
 
 	if wrapper.configPath != "" || len(options.Env) > 0 {
 		cmd.Env = os.Environ()