diff --git a/pkg/cortex/modules.go b/pkg/cortex/modules.go
index 9e72894f9e..9489fab2ec 100644
--- a/pkg/cortex/modules.go
+++ b/pkg/cortex/modules.go
@@ -160,6 +160,20 @@ func (t *Cortex) initRuntimeConfig() (services.Service, error) {
 	registerer := prometheus.WrapRegistererWithPrefix("cortex_", prometheus.DefaultRegisterer)
 	logger := util_log.Logger
 	bucketClientFactory := func(ctx context.Context) (objstore.Bucket, error) {
+		// When directory is an empty string but the runtime-config.file is an absolute path,
+		// the filesystem.NewBucketClient will treat it as a relative path based on the current working directory
+		// that the process is running in.
+		if t.Cfg.RuntimeConfig.StorageConfig.Backend == bucket.Filesystem {
+			if t.Cfg.RuntimeConfig.StorageConfig.Filesystem.Directory == "" {
+				// Check if runtime-config.file is an absolute path
+				if t.Cfg.RuntimeConfig.LoadPath[0] == '/' {
+					// If it is, set the directory to the root directory so that the filesystem bucket
+					// will treat it as an absolute path. This is to maintain backwards compatibility
+					// with the previous behavior of the runtime-config.file of allowing relative and absolute paths.
+					t.Cfg.RuntimeConfig.StorageConfig.Filesystem.Directory = "/"
+				}
+			}
+		}
 		return bucket.NewClient(ctx, t.Cfg.RuntimeConfig.StorageConfig, "runtime-config", logger, registerer)
 	}
 	serv, err := runtimeconfig.New(t.Cfg.RuntimeConfig, registerer, logger, bucketClientFactory)