diff --git a/src/duckstation-qt/autoupdaterdialog.cpp b/src/duckstation-qt/autoupdaterdialog.cpp
index 9e1dce0d3..bd018be3d 100644
--- a/src/duckstation-qt/autoupdaterdialog.cpp
+++ b/src/duckstation-qt/autoupdaterdialog.cpp
@@ -256,6 +256,7 @@ void AutoUpdaterDialog::getChangesComplete(QNetworkReply* reply)
 
       const QJsonArray commits(doc_object["commits"].toArray());
       bool update_will_break_save_states = false;
+      bool update_increases_settings_version = false;
 
       for (const QJsonValue& commit : commits)
       {
@@ -274,6 +275,9 @@ void AutoUpdaterDialog::getChangesComplete(QNetworkReply* reply)
 
         if (message.contains(QStringLiteral("[SAVEVERSION+]")))
           update_will_break_save_states = true;
+        
+        if (message.contains(QStringLiteral("[SETTINGSVERSION+]")))
+          update_increases_settings_version = true;
       }
 
       changes_html += "</ul>";
@@ -285,6 +289,13 @@ void AutoUpdaterDialog::getChangesComplete(QNetworkReply* reply)
                                 "before installing this update or you will lose progress.</p>"));
       }
 
+      if (update_increases_settings_version)
+      {
+        changes_html.prepend(
+          tr("<h2>Settings Warning</h2><p>Installing this update will reset your program configuration. Please note "
+             "that you will have to reconfigure your settings after this update.</p>"));
+      }
+
       changes_html += tr("<h4>Installing this update will download %1 MB through your internet connection.</h4>")
                         .arg(static_cast<double>(m_download_size) / 1000000.0, 0, 'f', 2);
 
diff --git a/src/duckstation-qt/main.cpp b/src/duckstation-qt/main.cpp
index 66bf4bf51..92a8f03da 100644
--- a/src/duckstation-qt/main.cpp
+++ b/src/duckstation-qt/main.cpp
@@ -55,6 +55,8 @@ int main(int argc, char* argv[])
     window->startupUpdateCheck();
   }
 
+  window->reportSettingsVersionMismatchString();
+
   int result = app.exec();
 
   window.reset();
diff --git a/src/duckstation-qt/mainwindow.cpp b/src/duckstation-qt/mainwindow.cpp
index 09ea254bf..ada85e362 100644
--- a/src/duckstation-qt/mainwindow.cpp
+++ b/src/duckstation-qt/mainwindow.cpp
@@ -1088,6 +1088,13 @@ void MainWindow::startupUpdateCheck()
   checkForUpdates(false);
 }
 
+void MainWindow::reportSettingsVersionMismatchString()
+{
+  const QString mismatch_str = QString::fromStdString(m_host_interface->GetSettingsVersionMismatchString());
+  if (!mismatch_str.isEmpty())
+    reportError(mismatch_str);
+}
+
 void MainWindow::updateDebugMenuVisibility()
 {
   const bool visible = m_host_interface->GetBoolSettingValue("Main", "ShowDebugMenu", false);
diff --git a/src/duckstation-qt/mainwindow.h b/src/duckstation-qt/mainwindow.h
index 3dc7c83cf..85e9b6137 100644
--- a/src/duckstation-qt/mainwindow.h
+++ b/src/duckstation-qt/mainwindow.h
@@ -30,6 +30,10 @@ public:
   /// Performs update check if enabled in settings.
   void startupUpdateCheck();
 
+  /// Reports m_host_interface's settings version mismatch string. Does nothing if string is empty (no settings version
+  /// mismatch detected).
+  void reportSettingsVersionMismatchString();
+
 public Q_SLOTS:
   /// Updates debug menu visibility (hides if disabled).
   void updateDebugMenuVisibility();
diff --git a/src/frontend-common/common_host_interface.cpp b/src/frontend-common/common_host_interface.cpp
index 5579d36de..499525347 100644
--- a/src/frontend-common/common_host_interface.cpp
+++ b/src/frontend-common/common_host_interface.cpp
@@ -1995,8 +1995,10 @@ void CommonHostInterface::CheckSettings(SettingsInterface& si)
   if (settings_version == SETTINGS_VERSION)
     return;
 
-  ReportFormattedError("Settings version %d does not match expected version %d, resetting", settings_version,
-                       SETTINGS_VERSION);
+  m_settings_version_mismatch_str = StringUtil::StdStringFromFormat(
+    "Settings version %d does not match expected version %d, resetting", settings_version, SETTINGS_VERSION);
+  ReportError(m_settings_version_mismatch_str.c_str());
+
   si.Clear();
   si.SetIntValue("Main", "SettingsVersion", SETTINGS_VERSION);
   SetDefaultSettings(si);
@@ -2101,6 +2103,11 @@ void CommonHostInterface::CheckForSettingsChanges(const Settings& old_settings)
   UpdateInputMap();
 }
 
+const std::string& CommonHostInterface::GetSettingsVersionMismatchString() const
+{
+  return m_settings_version_mismatch_str;
+}
+
 void CommonHostInterface::SetTimerResolutionIncreased(bool enabled)
 {
   if (m_timer_resolution_increased == enabled)
diff --git a/src/frontend-common/common_host_interface.h b/src/frontend-common/common_host_interface.h
index e21a6b92d..07ad70d97 100644
--- a/src/frontend-common/common_host_interface.h
+++ b/src/frontend-common/common_host_interface.h
@@ -174,6 +174,10 @@ public:
   /// Reloads post processing shaders with the current configuration.
   void ReloadPostProcessingShaders();
 
+  /// Returns an empty string if no settings version mismatch was detected, non-empty otherwise. Should not be called
+  /// before CheckSettings(SettingsInterface& si).
+  const std::string& GetSettingsVersionMismatchString() const;
+
 protected:
   enum : u32
   {
@@ -371,6 +375,8 @@ private:
   // running in batch mode? i.e. exit after stopping emulation
   bool m_batch_mode = false;
 
+  std::string m_settings_version_mismatch_str;
+
 #ifdef WITH_DISCORD_PRESENCE
   // discord rich presence
   bool m_discord_presence_enabled = false;