diff --git a/src/cloneCommand.tsx b/src/cloneCommand.tsx
index 28484a7e9..12efa6ae1 100644
--- a/src/cloneCommand.tsx
+++ b/src/cloneCommand.tsx
@@ -69,7 +69,9 @@ export const gitCloneCommandPlugin: JupyterFrontEndPlugin<void> = {
               Operation.Clone,
               trans,
               {
-                path: fileBrowserModel.path,
+                path: app.serviceManager.contents.localPath(
+                  fileBrowserModel.path
+                ),
                 url: result.value.url,
                 versioning: result.value.versioning,
                 submodules: result.value.submodules
@@ -125,7 +127,13 @@ export const gitCloneCommandPlugin: JupyterFrontEndPlugin<void> = {
     );
 
     // Add the context menu items for the default file browser
-    addFileBrowserContextMenu(gitModel, fileBrowser, app.contextMenu, trans);
+    addFileBrowserContextMenu(
+      gitModel,
+      fileBrowser,
+      app.serviceManager.contents,
+      app.contextMenu,
+      trans
+    );
 
     if (palette) {
       // Add the commands to the command palette
diff --git a/src/commandsAndMenu.tsx b/src/commandsAndMenu.tsx
index 61ffbeefd..dbf0c58a3 100644
--- a/src/commandsAndMenu.tsx
+++ b/src/commandsAndMenu.tsx
@@ -210,7 +210,9 @@ export function addCommands(
       'Create an empty Git repository or reinitialize an existing one'
     ),
     execute: async () => {
-      const currentPath = fileBrowserModel.path;
+      const currentPath = app.serviceManager.contents.localPath(
+        fileBrowserModel.path
+      );
       const result = await showDialog({
         title: trans.__('Initialize a Repository'),
         body: trans.__('Do you really want to make this directory a Git Repo?'),
@@ -1314,7 +1316,9 @@ export function addCommands(
                 change.newValue?.last_modified ?? 0
               ).valueOf();
               if (
-                change.newValue?.path === fullPath &&
+                app.serviceManager.contents.localPath(
+                  change.newValue?.path ?? ''
+                ) === fullPath &&
                 model.challenger.updateAt !== updateAt
               ) {
                 model.challenger = {
@@ -1794,6 +1798,7 @@ export function addHistoryMenuItems(
 export function addFileBrowserContextMenu(
   model: IGitExtension,
   filebrowser: FileBrowser,
+  contents: Contents.IManager,
   contextMenu: ContextMenuSvg,
   trans: TranslationBundle
 ): void {
@@ -1809,11 +1814,12 @@ export function addFileBrowserContextMenu(
     const statuses = new Set<Git.Status>(
       // @ts-expect-error file cannot be undefined or null
       items
-        .map(item =>
-          model.pathRepository === null
+        .map(item => {
+          const itemPath = contents.localPath(item.path);
+          return model.pathRepository === null
             ? undefined
-            : model.getFile(item.path)?.status
-        )
+            : model.getFile(itemPath)?.status;
+        })
         .filter(status => typeof status !== 'undefined')
     );
 
diff --git a/src/index.ts b/src/index.ts
index 928032747..7e0729136 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -147,19 +147,25 @@ async function activate(
   // Create the Git model
   const gitExtension = new GitExtension(docmanager, app.docRegistry, settings);
 
-  // Whenever we restore the application, sync the Git extension path
-  Promise.all([app.restored, fileBrowser.model.restored]).then(() => {
-    gitExtension.pathRepository = fileBrowser.model.path;
-  });
-
   const onPathChanged = (
     model: FileBrowserModel,
     change: IChangedArgs<string>
   ) => {
-    gitExtension.pathRepository = change.newValue;
+    gitExtension.pathRepository = app.serviceManager.contents.localPath(
+      change.newValue
+    );
     gitExtension.refreshBranch();
   };
 
+  // Whenever we restore the application, sync the Git extension path
+  Promise.all([app.restored, fileBrowser.model.restored]).then(() => {
+    onPathChanged(fileBrowser.model, {
+      name: 'path',
+      newValue: fileBrowser.model.path,
+      oldValue: ''
+    });
+  });
+
   // Whenever the file browser path changes, sync the Git extension path
   fileBrowser.model.pathChanged.connect(onPathChanged);
 
@@ -245,6 +251,7 @@ async function activate(
     addFileBrowserContextMenu(
       gitExtension,
       fileBrowser,
+      app.serviceManager.contents,
       app.contextMenu,
       trans
     );