diff --git a/packages/melos/lib/src/commands/bootstrap.dart b/packages/melos/lib/src/commands/bootstrap.dart
index 00c43090..887f6f35 100644
--- a/packages/melos/lib/src/commands/bootstrap.dart
+++ b/packages/melos/lib/src/commands/bootstrap.dart
@@ -332,6 +332,14 @@ mixin _BootstrapMixin on _CleanMixin {
     return didUpdate;
   }
 
+  bool _areDependenciesEqual(DependencyReference? a, DependencyReference? b) {
+    if (a is GitReference && b is GitReference) {
+      return a == b && a.path == b.path;
+    } else {
+      return a == b;
+    }
+  }
+
   int _updateDependencies({
     required YamlEditor pubspecEditor,
     required Map<String, DependencyReference>? workspaceDependencies,
@@ -343,7 +351,9 @@ mixin _BootstrapMixin on _CleanMixin {
     // dependencies that have a different version specified in the workspace.
     final dependenciesToUpdate = workspaceDependencies.entries.where((entry) {
       if (!packageDependencies.containsKey(entry.key)) return false;
-      if (packageDependencies[entry.key] == entry.value) return false;
+      if (_areDependenciesEqual(packageDependencies[entry.key], entry.value)) {
+        return false;
+      }
       return true;
     });