diff --git a/src/UpdateScripts/UpdateGlobalVariables.php b/src/UpdateScripts/UpdateGlobalVariables.php
index 414261c2bc5..8fe0755f904 100644
--- a/src/UpdateScripts/UpdateGlobalVariables.php
+++ b/src/UpdateScripts/UpdateGlobalVariables.php
@@ -76,7 +76,7 @@ private function migrateFileStructure(): void
 
             $globalSet->save();
 
-            File::put($variablesPath, YAML::dump($data));
+            $globalSet->inDefaultSite()->data($data)->saveQuietly();
         });
     }
 }
diff --git a/tests/UpdateScripts/UpdateGlobalVariablesTest.php b/tests/UpdateScripts/UpdateGlobalVariablesTest.php
index 2cc3fc6bf21..9d74711bc03 100644
--- a/tests/UpdateScripts/UpdateGlobalVariablesTest.php
+++ b/tests/UpdateScripts/UpdateGlobalVariablesTest.php
@@ -4,6 +4,7 @@
 
 use Illuminate\Support\Facades\File;
 use PHPUnit\Framework\Attributes\Test;
+use Statamic\Facades\GlobalSet;
 use Statamic\Facades\YAML;
 use Statamic\UpdateScripts\UpdateGlobalVariables;
 use Tests\PreventSavingStacheItemsToDisk;
@@ -79,6 +80,32 @@ public function it_migrates_global_variables_with_empty_data_in_a_single_site_in
         unlink($this->globalsPath.'/en/test.yaml');
     }
 
+    #[Test]
+    public function migrated_variables_survive_being_saved_later_in_the_same_process()
+    {
+        File::put($this->globalsPath.'/test.yaml', Yaml::dump([
+            'title' => 'Test',
+            'data' => [
+                'foo' => 'Bar',
+            ],
+        ]));
+
+        $this->runUpdateScript(UpdateGlobalVariables::class);
+
+        // Simulates an addon update script saving variables after the migration
+        $variables = GlobalSet::findByHandle('test')->inDefaultSite();
+        $variables->set('baz', 'Qux');
+        $variables->save();
+
+        $this->assertEquals(
+            ['foo' => 'Bar', 'baz' => 'Qux'],
+            YAML::parse(File::get($this->globalsPath.'/en/test.yaml'))
+        );
+
+        unlink($this->globalsPath.'/test.yaml');
+        unlink($this->globalsPath.'/en/test.yaml');
+    }
+
     #[Test]
     public function it_builds_the_sites_array_in_a_multi_site_install()
     {