diff --git a/.changes/fix-wix-upgrade.md b/.changes/fix-wix-upgrade.md
new file mode 100644
index 000000000..b2317a69b
--- /dev/null
+++ b/.changes/fix-wix-upgrade.md
@@ -0,0 +1,5 @@
+---
+"tauri-bundler": patch
+---
+
+Fixes lost files on upgrade due to wrong implementation to keep shortcuts.
diff --git a/tooling/bundler/src/bundle/windows/templates/main.wxs b/tooling/bundler/src/bundle/windows/templates/main.wxs
index 779c24161..7ea8a7211 100644
--- a/tooling/bundler/src/bundle/windows/templates/main.wxs
+++ b/tooling/bundler/src/bundle/windows/templates/main.wxs
@@ -30,11 +30,15 @@
         <Property Id="REINSTALLMODE" Value="dmus" />
 
         {{#if allow_downgrades}}
-            <MajorUpgrade AllowDowngrades="yes" Schedule="afterInstallExecute" />
+            <MajorUpgrade AllowDowngrades="yes" Schedule="afterInstallValidate" />
         {{else}}
             <MajorUpgrade DowngradeErrorMessage="!(loc.DowngradeErrorMessage)" AllowSameVersionUpgrades="yes" />
         {{/if}}
 
+        <InstallExecuteSequence>
+            <RemoveShortcuts>Installed AND NOT UPGRADINGPRODUCTCODE</RemoveShortcuts>
+        </InstallExecuteSequence>
+
         <Media Id="1" Cabinet="app.cab" EmbedCab="yes" />
 
         {{#if banner_path}}