diff --git a/pkg/admin/prerun/prerun.go b/pkg/admin/prerun/prerun.go
index f8718e980a..44a2b049a6 100644
--- a/pkg/admin/prerun/prerun.go
+++ b/pkg/admin/prerun/prerun.go
@@ -55,17 +55,17 @@ func (pr *PreRun) Perform() error {
 		return nil
 	}
 
-	dataExists, err := util.PathExists(config.DataDir)
+	dataExists, err := util.PathExistsAndIsNotEmpty(config.DataDir, ".nodename")
 	if err != nil {
 		return fmt.Errorf("failed to check if data directory already exists: %w", err)
 	}
 
-	versionExists, err := util.PathExists(versionFilePath)
+	versionExists, err := util.PathExistsAndIsNotEmpty(versionFilePath)
 	if err != nil {
 		return fmt.Errorf("checking if version metadata exists failed: %w", err)
 	}
 
-	healthExists, err := util.PathExists(healthFilepath)
+	healthExists, err := util.PathExistsAndIsNotEmpty(healthFilepath)
 	if err != nil {
 		return fmt.Errorf("failed to check if health file already exists: %w", err)
 	}
@@ -363,7 +363,7 @@ func getCurrentBootID() (string, error) {
 }
 
 func getHealthInfo() (*HealthInfo, error) {
-	if exists, err := util.PathExists(healthFilepath); err != nil {
+	if exists, err := util.PathExistsAndIsNotEmpty(healthFilepath); err != nil {
 		return nil, err
 	} else if !exists {
 		return nil, errHealthFileDoesNotExist
diff --git a/pkg/admin/prerun/version.go b/pkg/admin/prerun/version.go
index c6ca61103a..3219a139e3 100644
--- a/pkg/admin/prerun/version.go
+++ b/pkg/admin/prerun/version.go
@@ -101,7 +101,7 @@ func getVersionOfExecutable() (versionMetadata, error) {
 }
 
 func getVersionOfData() (versionMetadata, error) {
-	exists, err := util.PathExists(versionFilePath)
+	exists, err := util.PathExistsAndIsNotEmpty(versionFilePath)
 	if err != nil {
 		return versionMetadata{}, fmt.Errorf("checking if path exists failed: %w", err)
 	}
diff --git a/pkg/util/util.go b/pkg/util/util.go
index e7fb5d787d..b1077c8aaf 100644
--- a/pkg/util/util.go
+++ b/pkg/util/util.go
@@ -4,6 +4,8 @@ import (
 	"errors"
 	"fmt"
 	"os"
+
+	"k8s.io/apimachinery/pkg/util/sets"
 )
 
 func Must(err error) {
@@ -32,3 +34,33 @@ func PathExists(path string) (bool, error) {
 func MakeDir(path string) error {
 	return os.MkdirAll(path, 0700)
 }
+
+func PathExistsAndIsNotEmpty(path string, ignores ...string) (bool, error) {
+	fi, err := os.Stat(path)
+	if err != nil {
+		if errors.Is(err, os.ErrNotExist) {
+			return false, nil
+		} else {
+			return false, fmt.Errorf("checking if path (%s) exists failed: %w", path, err)
+		}
+	}
+
+	if !fi.IsDir() {
+		return fi.Size() != 0, nil
+	}
+
+	files, err := os.ReadDir(path)
+	if err != nil {
+		return false, fmt.Errorf("failed to ReadDir %q: %w", path, err)
+	}
+
+	iset := sets.New[string](ignores...)
+	for _, f := range files {
+		if iset.Has(f.Name()) {
+			continue
+		}
+		return true, nil
+	}
+
+	return false, nil
+}