diff --git a/packages/orchestrator/pkg/template/build/commands/workdir.go b/packages/orchestrator/pkg/template/build/commands/workdir.go
index 592754b89a..4029443b45 100644
--- a/packages/orchestrator/pkg/template/build/commands/workdir.go
+++ b/packages/orchestrator/pkg/template/build/commands/workdir.go
@@ -102,34 +102,53 @@ func saveWorkdirMeta(
 	cmdMetadata metadata.Context,
 	workdir string,
 ) (m metadata.Context, e error) {
-	var outputErr error
+	var stdout strings.Builder
+	var stderr strings.Builder
 	err := sandboxtools.RunCommandWithOutput(
 		ctx,
 		proxy,
 		sandboxID,
-		fmt.Sprintf(`cd "%s" && pwd`, workdir),
+		fmt.Sprintf(`cd "%s" && printf '\n%s%%s\n' "$PWD"`, workdir, workdirOutputMarker),
 		metadata.Context{
-			User: "root",
+			User:    "root",
+			EnvVars: cmdMetadata.EnvVars,
 			// Workdir can't be set here to not error when current workdir is deleted
 		},
-		func(stdout, stderr string) {
-			if stderr != "" {
-				outputErr = fmt.Errorf("error getting absolute path of workdir: %s", stderr)
-
-				return
-			}
-			workdir = strings.TrimSpace(stdout)
+		func(out, errOut string) {
+			_, _ = stdout.WriteString(out)
+			_, _ = stderr.WriteString(errOut)
 		},
 	)
-	if outputErr != nil {
-		return metadata.Context{}, outputErr
-	}
+	return saveWorkdirMetaFromOutput(cmdMetadata, workdir, stdout.String(), stderr.String(), err)
+}
+
+const workdirOutputMarker = "__E2B_WORKDIR__:"
 
+func saveWorkdirMetaFromOutput(
+	cmdMetadata metadata.Context,
+	workdir, stdout, stderr string,
+	commandErr error,
+) (metadata.Context, error) {
+	resolved, err := absoluteWorkdirFromOutput(stdout, stderr, commandErr)
 	if err != nil {
 		return metadata.Context{}, fmt.Errorf("failed to save workdir %s: %w", workdir, err)
 	}
-
-	cmdMetadata.WorkDir = &workdir
-
+	cmdMetadata.WorkDir = &resolved
 	return cmdMetadata, nil
 }
+
+// absoluteWorkdirFromOutput uses a marked line so unrelated login-hook output
+// cannot be mistaken for pwd. The caller collects all stream chunks first.
+func absoluteWorkdirFromOutput(stdout, stderr string, commandErr error) (string, error) {
+	if commandErr != nil {
+		return "", fmt.Errorf("workdir command failed: %w", commandErr)
+	}
+	marker := strings.LastIndex(stdout, workdirOutputMarker)
+	if marker >= 0 {
+		path := strings.TrimSpace(strings.SplitN(stdout[marker+len(workdirOutputMarker):], "\n", 2)[0])
+		if filepath.IsAbs(path) {
+			return path, nil
+		}
+	}
+	return "", fmt.Errorf("error getting absolute path of workdir: stdout=%q stderr=%q", stdout, stderr)
+}
diff --git a/packages/orchestrator/pkg/template/build/commands/workdir_parse_test.go b/packages/orchestrator/pkg/template/build/commands/workdir_parse_test.go
new file mode 100644
index 0000000000..ecfe91b71a
--- /dev/null
+++ b/packages/orchestrator/pkg/template/build/commands/workdir_parse_test.go
@@ -0,0 +1,61 @@
+package commands
+
+import (
+	"errors"
+	"reflect"
+	"strings"
+	"testing"
+
+	"github.com/e2b-dev/infra/packages/orchestrator/pkg/template/metadata"
+)
+
+func TestSaveWorkdirMetaFromOutputPreservesImageMetadata(t *testing.T) {
+	oldWorkdir := "/image-default"
+	envs := map[string]string{"MAMBA_EXE": "/bin/micromamba", "APP_MODE": "freecad"}
+	image := metadata.Context{User: "app-user", WorkDir: &oldWorkdir, EnvVars: envs}
+
+	got, err := saveWorkdirMetaFromOutput(
+		image,
+		"/app",
+		"login hook stdout: /noise/path\n"+workdirOutputMarker+"/app\n",
+		"_activate_current_env.sh: line 8: : command not found\ncritical libmamba Shell not initialized\n",
+		nil,
+	)
+	if err != nil {
+		t.Fatalf("unexpected error: %v", err)
+	}
+	if got.User != image.User {
+		t.Fatalf("user changed: got %q want %q", got.User, image.User)
+	}
+	if !reflect.DeepEqual(got.EnvVars, image.EnvVars) {
+		t.Fatalf("environment changed: got %#v want %#v", got.EnvVars, image.EnvVars)
+	}
+	if got.WorkDir == nil || *got.WorkDir != "/app" {
+		t.Fatalf("got workdir %v want /app", got.WorkDir)
+	}
+	if image.WorkDir == nil || *image.WorkDir != oldWorkdir {
+		t.Fatalf("input metadata was mutated: %#v", image)
+	}
+}
+
+func TestSaveWorkdirMetaFromOutputRejectsMissingAbsolutePath(t *testing.T) {
+	_, err := saveWorkdirMetaFromOutput(
+		metadata.Context{}, "/app", "hook output only", "login hook diagnostic", nil,
+	)
+	if err == nil {
+		t.Fatal("expected an error without an absolute marked path")
+	}
+	if !strings.Contains(err.Error(), "login hook diagnostic") {
+		t.Fatalf("error omits stderr context: %v", err)
+	}
+}
+
+func TestSaveWorkdirMetaFromOutputPreservesCommandFailure(t *testing.T) {
+	commandErr := errors.New("exit status 1")
+	_, err := saveWorkdirMetaFromOutput(
+		metadata.Context{}, "/app", workdirOutputMarker+"/app\n", "", commandErr,
+	)
+	if !errors.Is(err, commandErr) {
+		t.Fatalf("got %v, want wrapped command error", err)
+	}
+}