diff --git a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/fragments/EmulationFragment.kt b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/fragments/EmulationFragment.kt
index e4698ba43c..e0efc43611 100644
--- a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/fragments/EmulationFragment.kt
+++ b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/fragments/EmulationFragment.kt
@@ -119,7 +119,10 @@ class EmulationFragment : Fragment(), SurfaceHolder.Callback {
     }
 
     override fun onDetach() {
-        NativeLibrary.clearEmulationActivity()
+        // Don't clear the reference if a newer EmulationActivity already took over
+        if (NativeLibrary.getEmulationActivity() === emulationActivity) {
+            NativeLibrary.clearEmulationActivity()
+        }
         super.onDetach()
     }
 
@@ -154,7 +157,10 @@ class EmulationFragment : Fragment(), SurfaceHolder.Callback {
 
     override fun surfaceDestroyed(holder: SurfaceHolder) {
         Log.debug("[EmulationFragment] Surface destroyed.")
-        NativeLibrary.SurfaceDestroyed()
+        // Don't tear down the surface if a newer EmulationActivity already took over
+        if (NativeLibrary.getEmulationActivity() === emulationActivity) {
+            NativeLibrary.SurfaceDestroyed()
+        }
         runWhenSurfaceIsValid = true
     }
 
diff --git a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/ui/main/MainActivity.kt b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/ui/main/MainActivity.kt
index 761c6dbfef..d61f1097c8 100644
--- a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/ui/main/MainActivity.kt
+++ b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/ui/main/MainActivity.kt
@@ -2,6 +2,7 @@
 
 package org.dolphinemu.dolphinemu.ui.main
 
+import android.content.Intent
 import android.content.pm.PackageManager
 import android.os.Bundle
 import android.view.Menu
@@ -90,6 +91,12 @@ class MainActivity : AppCompatActivity(), MainView, OnRefreshListener, ThemeProv
         }
     }
 
+    override fun onNewIntent(intent: Intent) {
+        super.onNewIntent(intent)
+        setIntent(intent)
+        StartupHandler.HandleInit(this)
+    }
+
     override fun onResume() {
         ThemeHelper.setCorrectTheme(this)
 
diff --git a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/ui/main/TvMainActivity.kt b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/ui/main/TvMainActivity.kt
index 09bacd201b..2cd8288eb4 100644
--- a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/ui/main/TvMainActivity.kt
+++ b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/ui/main/TvMainActivity.kt
@@ -66,6 +66,12 @@ class TvMainActivity : FragmentActivity(), MainView, OnRefreshListener {
         }
     }
 
+    override fun onNewIntent(intent: Intent) {
+        super.onNewIntent(intent)
+        setIntent(intent)
+        StartupHandler.HandleInit(this)
+    }
+
     override fun onResume() {
         super.onResume()
         if (DirectoryInitialization.shouldStart(this)) {
diff --git a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/utils/StartupHandler.java b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/utils/StartupHandler.java
index db003b82b2..775e8a3330 100644
--- a/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/utils/StartupHandler.java
+++ b/Source/Android/app/src/main/java/org/dolphinemu/dolphinemu/utils/StartupHandler.java
@@ -9,7 +9,10 @@ import android.content.Intent;
 import android.content.SharedPreferences;
 import android.net.Uri;
 import android.os.Bundle;
+import android.os.Handler;
+import android.os.Looper;
 import android.text.TextUtils;
+import android.util.Log;
 
 import androidx.fragment.app.FragmentActivity;
 import androidx.lifecycle.LifecycleOwner;
@@ -38,11 +41,44 @@ public final class StartupHandler
     String[] gamesToLaunch = getGamesFromIntent(parent.getIntent());
     if (gamesToLaunch != null && gamesToLaunch.length > 0)
     {
-      // Start the emulation activity, send the ISO passed in and finish the main activity
-      EmulationActivity.launch(parent, gamesToLaunch, false, true);
+      // If a previous session is still running, stop it and wait for it to finish
+      // before launching the new game. StopEmulation is async, so launching immediately
+      // would race with the old emulation thread's cleanup.
+      if (!NativeLibrary.IsUninitialized())
+      {
+        NativeLibrary.StopEmulation();
+        waitForStopThenLaunch(parent, gamesToLaunch);
+      }
+      else
+      {
+        EmulationActivity.stopIgnoringLaunchRequests();
+        EmulationActivity.launch(parent, gamesToLaunch, false, true);
+      }
     }
   }
 
+  private static void waitForStopThenLaunch(FragmentActivity parent, String[] gamesToLaunch)
+  {
+    Handler handler = new Handler(Looper.getMainLooper());
+    final long deadline = System.currentTimeMillis() + 5000;
+    handler.postDelayed(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        if (NativeLibrary.IsUninitialized() || System.currentTimeMillis() >= deadline)
+        {
+          EmulationActivity.stopIgnoringLaunchRequests();
+          EmulationActivity.launch(parent, gamesToLaunch, false, true);
+        }
+        else
+        {
+          handler.postDelayed(this, 100);
+        }
+      }
+    }, 100);
+  }
+
   private static String[] getGamesFromIntent(Intent intent)
   {
     // Priority order when looking for game paths in an intent: