diff --git a/src/android/app/src/main/java/org/yuzu/yuzu_emu/activities/EmulationActivity.kt b/src/android/app/src/main/java/org/yuzu/yuzu_emu/activities/EmulationActivity.kt
index 2764d7eac6..44290fd4b6 100644
--- a/src/android/app/src/main/java/org/yuzu/yuzu_emu/activities/EmulationActivity.kt
+++ b/src/android/app/src/main/java/org/yuzu/yuzu_emu/activities/EmulationActivity.kt
@@ -25,6 +25,11 @@ import android.hardware.SensorEventListener
 import android.hardware.SensorManager
 import android.os.Build
 import android.os.Bundle
+import android.os.Handler
+import android.os.Looper
+import androidx.navigation.NavOptions
+import org.yuzu.yuzu_emu.fragments.EmulationFragment
+import org.yuzu.yuzu_emu.utils.CustomSettingsHandler
 import android.util.Rational
 import android.view.InputDevice
 import android.view.KeyEvent
@@ -87,6 +92,28 @@ class EmulationActivity : AppCompatActivity(), SensorEventListener, InputManager
     private val emulationViewModel: EmulationViewModel by viewModels()
 
     private var foregroundService: Intent? = null
+    private val mainHandler = Handler(Looper.getMainLooper())
+    private var pendingRomSwapIntent: Intent? = null
+    private var isWaitingForRomSwapStop = false
+    private var romSwapNativeStopped = false
+    private var romSwapThreadStopped = false
+    private var romSwapGeneration = 0
+    private var hasEmulationSession = processHasEmulationSession
+    private val romSwapStopTimeoutRunnable = Runnable { onRomSwapStopTimeout() }
+
+    private fun onRomSwapStopTimeout() {
+        if (!isWaitingForRomSwapStop) {
+            return
+        }
+        Log.warning("[EmulationActivity] ROM swap stop timed out; retrying native stop and continuing to wait")
+        NativeLibrary.stopEmulation()
+        scheduleRomSwapStopTimeout()
+    }
+
+    private fun scheduleRomSwapStopTimeout() {
+        mainHandler.removeCallbacks(romSwapStopTimeoutRunnable)
+        mainHandler.postDelayed(romSwapStopTimeoutRunnable, ROM_SWAP_STOP_TIMEOUT_MS)
+    }
 
     override fun attachBaseContext(base: Context) {
         super.attachBaseContext(YuzuApplication.applyLanguage(base))
@@ -128,9 +155,29 @@ class EmulationActivity : AppCompatActivity(), SensorEventListener, InputManager
         binding = ActivityEmulationBinding.inflate(layoutInflater)
         setContentView(binding.root)
 
+        val launchIntent = Intent(intent)
+        val shouldDeferLaunchForSwap = hasEmulationSession && isSwapIntent(launchIntent)
+        if (shouldDeferLaunchForSwap) {
+            Log.info("[EmulationActivity] onCreate detected existing session; deferring new game setup for swap")
+            emulationViewModel.setIsEmulationStopping(true)
+            emulationViewModel.setEmulationStopped(false)
+        }
+
         val navHostFragment =
             supportFragmentManager.findFragmentById(R.id.fragment_container) as NavHostFragment
-        navHostFragment.navController.setGraph(R.navigation.emulation_navigation, intent.extras)
+        val initialArgs = if (shouldDeferLaunchForSwap) {
+            Bundle(intent.extras ?: Bundle()).apply {
+                processSessionGame?.let { putParcelable("game", it) }
+            }
+        } else {
+            intent.extras
+        }
+        navHostFragment.navController.setGraph(R.navigation.emulation_navigation, initialArgs)
+        if (shouldDeferLaunchForSwap) {
+            mainHandler.post {
+                handleSwapIntent(launchIntent)
+            }
+        }
 
         isActivityRecreated = savedInstanceState != null
 
@@ -210,6 +257,7 @@ class EmulationActivity : AppCompatActivity(), SensorEventListener, InputManager
     }
 
     override fun onDestroy() {
+        mainHandler.removeCallbacks(romSwapStopTimeoutRunnable)
         super.onDestroy()
         inputManager.unregisterInputDeviceListener(this)
         stopForegroundService(this)
@@ -228,15 +276,121 @@ class EmulationActivity : AppCompatActivity(), SensorEventListener, InputManager
 
     override fun onNewIntent(intent: Intent) {
         super.onNewIntent(intent)
-        setIntent(intent)
+        handleSwapIntent(intent)
+        nfcReader.onNewIntent(intent)
+        InputHandler.updateControllerData()
+    }
+
+    private fun isSwapIntent(intent: Intent): Boolean {
+        return when {
+            intent.getBooleanExtra(EXTRA_OVERLAY_GAMELESS_EDIT_MODE, false) -> false
+            intent.action == CustomSettingsHandler.CUSTOM_CONFIG_ACTION -> true
+            intent.data != null -> true
+            else -> {
+                val extras = intent.extras
+                extras != null &&
+                    BundleCompat.getParcelable(extras, EXTRA_SELECTED_GAME, Game::class.java) != null
+            }
+        }
+    }
 
-        // Reset navigation graph with new intent data to recreate EmulationFragment
+    private fun handleSwapIntent(intent: Intent) {
+        if (!isSwapIntent(intent)) {
+            return
+        }
+
+            pendingRomSwapIntent = Intent(intent)
+
+            if (!isWaitingForRomSwapStop) {
+                Log.info("[EmulationActivity] Begin ROM swap: data=${intent.data}")
+                isWaitingForRomSwapStop = true
+                romSwapNativeStopped = false
+                romSwapThreadStopped = false
+                romSwapGeneration += 1
+                val thisSwapGeneration = romSwapGeneration
+                emulationViewModel.setIsEmulationStopping(true)
+                emulationViewModel.setEmulationStopped(false)
+                val navHostFragment =
+                    supportFragmentManager.findFragmentById(R.id.fragment_container) as? NavHostFragment
+                val childFragmentManager = navHostFragment?.childFragmentManager
+                val stoppingFragmentForSwap =
+                    (childFragmentManager?.primaryNavigationFragment as? EmulationFragment) ?:
+                    childFragmentManager
+                        ?.fragments
+                        ?.asReversed()
+                        ?.firstOrNull {
+                            it is EmulationFragment &&
+                                it.isAdded &&
+                            it.view != null &&
+                            !it.isRemoving
+                        } as? EmulationFragment
+
+                val hasSessionForSwap = hasEmulationSession || stoppingFragmentForSwap != null
+
+                if (!hasSessionForSwap) {
+                    romSwapNativeStopped = true
+                    romSwapThreadStopped = true
+                } else {
+                    if (stoppingFragmentForSwap != null) {
+                        stoppingFragmentForSwap.stopForRomSwap()
+                        stoppingFragmentForSwap.notifyWhenEmulationThreadStops {
+                            if (!isWaitingForRomSwapStop || romSwapGeneration != thisSwapGeneration) {
+                                return@notifyWhenEmulationThreadStops
+                            }
+                            romSwapThreadStopped = true
+                            Log.info("[EmulationActivity] ROM swap thread stop acknowledged")
+                            launchPendingRomSwap(force = false)
+                        }
+                    } else {
+                        Log.warning("[EmulationActivity] ROM swap stop target fragment not found; requesting native stop")
+                        romSwapThreadStopped = true
+                        NativeLibrary.stopEmulation()
+                    }
+
+                    scheduleRomSwapStopTimeout()
+                }
+            }
+
+            launchPendingRomSwap(force = false)
+    }
+
+    private fun launchPendingRomSwap(force: Boolean) {
+        if (!isWaitingForRomSwapStop) {
+            return
+        }
+        if (!force && (!romSwapNativeStopped || !romSwapThreadStopped)) {
+            return
+        }
+        val swapIntent = pendingRomSwapIntent ?: return
+        Log.info("[EmulationActivity] Launching pending ROM swap: data=${swapIntent.data}")
+        pendingRomSwapIntent = null
+        isWaitingForRomSwapStop = false
+        romSwapNativeStopped = false
+        romSwapThreadStopped = false
+        mainHandler.removeCallbacks(romSwapStopTimeoutRunnable)
+        applyGameLaunchIntent(swapIntent)
+    }
+
+    private fun applyGameLaunchIntent(intent: Intent) {
+        hasEmulationSession = true
+        processHasEmulationSession = true
+        emulationViewModel.setIsEmulationStopping(false)
+        emulationViewModel.setEmulationStopped(false)
+        setIntent(Intent(intent))
         val navHostFragment =
             supportFragmentManager.findFragmentById(R.id.fragment_container) as NavHostFragment
-        navHostFragment.navController.setGraph(R.navigation.emulation_navigation, intent.extras)
-
-        nfcReader.onNewIntent(intent)
-        InputHandler.updateControllerData()
+        val navController = navHostFragment.navController
+        val startArgs = intent.extras?.let { Bundle(it) } ?: Bundle()
+        val navOptions = NavOptions.Builder()
+            .setPopUpTo(R.id.emulationFragment, true)
+            .build()
+
+        runCatching {
+            navController.navigate(R.id.emulationFragment, startArgs, navOptions)
+        }.onFailure {
+            Log.warning("[EmulationActivity] ROM swap navigate fallback to setGraph: ${it.message}")
+            navController.setGraph(R.navigation.emulation_navigation, startArgs)
+        }
     }
 
     override fun dispatchKeyEvent(event: KeyEvent): Boolean {
@@ -608,19 +762,48 @@ class EmulationActivity : AppCompatActivity(), SensorEventListener, InputManager
     }
 
     fun onEmulationStarted() {
+        if (Looper.myLooper() != Looper.getMainLooper()) {
+            mainHandler.post { onEmulationStarted() }
+            return
+        }
+        hasEmulationSession = true
+        processHasEmulationSession = true
         emulationViewModel.setEmulationStarted(true)
+        emulationViewModel.setIsEmulationStopping(false)
+        emulationViewModel.setEmulationStopped(false)
         NativeLibrary.playTimeManagerStart()
 
     }
 
     fun onEmulationStopped(status: Int) {
-        if (status == 0 && emulationViewModel.programChanged.value == -1) {
+        if (Looper.myLooper() != Looper.getMainLooper()) {
+            mainHandler.post { onEmulationStopped(status) }
+            return
+        }
+        hasEmulationSession = false
+        processHasEmulationSession = false
+        if (isWaitingForRomSwapStop) {
+            romSwapNativeStopped = true
+            Log.info("[EmulationActivity] ROM swap native stop acknowledged")
+            launchPendingRomSwap(force = false)
+        } else if (status == 0 && emulationViewModel.programChanged.value == -1) {
+            processSessionGame = null
             finish()
+        } else if (!isWaitingForRomSwapStop) {
+            processSessionGame = null
         }
         emulationViewModel.setEmulationStopped(true)
     }
 
+    fun updateSessionGame(game: Game?) {
+        processSessionGame = game
+    }
+
     fun onProgramChanged(programIndex: Int) {
+        if (Looper.myLooper() != Looper.getMainLooper()) {
+            mainHandler.post { onProgramChanged(programIndex) }
+            return
+        }
         emulationViewModel.setProgramChanged(programIndex)
     }
 
@@ -644,6 +827,11 @@ class EmulationActivity : AppCompatActivity(), SensorEventListener, InputManager
     companion object {
         const val EXTRA_SELECTED_GAME = "SelectedGame"
         const val EXTRA_OVERLAY_GAMELESS_EDIT_MODE = "overlayGamelessEditMode"
+        private const val ROM_SWAP_STOP_TIMEOUT_MS = 5000L
+        @Volatile
+        private var processHasEmulationSession = false
+        @Volatile
+        private var processSessionGame: Game? = null
 
         fun stopForegroundService(activity: Activity) {
             val startIntent = Intent(activity, ForegroundService::class.java)
diff --git a/src/android/app/src/main/java/org/yuzu/yuzu_emu/fragments/EmulationFragment.kt b/src/android/app/src/main/java/org/yuzu/yuzu_emu/fragments/EmulationFragment.kt
index 435fe5fe2c..b67bc6a9cc 100644
--- a/src/android/app/src/main/java/org/yuzu/yuzu_emu/fragments/EmulationFragment.kt
+++ b/src/android/app/src/main/java/org/yuzu/yuzu_emu/fragments/EmulationFragment.kt
@@ -50,6 +50,7 @@ import androidx.fragment.app.Fragment
 import androidx.fragment.app.activityViewModels
 import androidx.lifecycle.lifecycleScope
 import androidx.navigation.findNavController
+import androidx.navigation.fragment.NavHostFragment
 import androidx.navigation.fragment.navArgs
 import androidx.window.layout.FoldingFeature
 import androidx.window.layout.WindowInfoTracker
@@ -135,6 +136,8 @@ class EmulationFragment : Fragment(), SurfaceHolder.Callback {
 
     private var intentGame: Game? = null
     private var isCustomSettingsIntent = false
+    private var isStoppingForRomSwap = false
+    private var deferGameSetupUntilStopCompletes = false
 
     private var perfStatsRunnable: Runnable? = null
     private var socRunnable: Runnable? = null
@@ -238,6 +241,14 @@ class EmulationFragment : Fragment(), SurfaceHolder.Callback {
             }
         }
 
+        if (emulationViewModel.isEmulationStopping.value) {
+            deferGameSetupUntilStopCompletes = true
+            if (game == null) {
+                game = args.game ?: intentGame
+            }
+            return
+        }
+
         finishGameSetup()
     }
 
@@ -260,6 +271,7 @@ class EmulationFragment : Fragment(), SurfaceHolder.Callback {
             }
 
             game = gameToUse
+            emulationActivity?.updateSessionGame(gameToUse)
         } catch (e: Exception) {
             Log.error("[EmulationFragment] Error during game setup: ${e.message}")
             Toast.makeText(
@@ -334,7 +346,8 @@ class EmulationFragment : Fragment(), SurfaceHolder.Callback {
         }
 
         emulationState = EmulationState(game!!.path) {
-            return@EmulationState driverViewModel.isInteractionAllowed.value
+            return@EmulationState driverViewModel.isInteractionAllowed.value &&
+                !isStoppingForRomSwap
         }
     }
 
@@ -890,8 +903,12 @@ class EmulationFragment : Fragment(), SurfaceHolder.Callback {
             }
         )
 
-        GameIconUtils.loadGameIcon(game!!, binding.loadingImage)
-        binding.loadingTitle.text = game!!.title
+        game?.let {
+            GameIconUtils.loadGameIcon(it, binding.loadingImage)
+            binding.loadingTitle.text = it.title
+        } ?: run {
+            binding.loadingTitle.text = ""
+        }
         binding.loadingTitle.isSelected = true
         binding.loadingText.isSelected = true
 
@@ -959,6 +976,12 @@ class EmulationFragment : Fragment(), SurfaceHolder.Callback {
                 ViewUtils.showView(binding.loadingIndicator)
                 ViewUtils.hideView(binding.inputContainer)
                 ViewUtils.hideView(binding.showStatsOverlayText)
+            } else if (deferGameSetupUntilStopCompletes) {
+                if (!isAdded) {
+                    return@collect
+                }
+                deferGameSetupUntilStopCompletes = false
+                finishGameSetup()
             }
         }
         emulationViewModel.drawerOpen.collect(viewLifecycleOwner) {
@@ -995,24 +1018,22 @@ class EmulationFragment : Fragment(), SurfaceHolder.Callback {
         }
 
         driverViewModel.isInteractionAllowed.collect(viewLifecycleOwner) {
-            if (it && !NativeLibrary.isRunning() && !NativeLibrary.isPaused()) {
-                startEmulation()
-            }
-        }
+            if (it &&
+                !isStoppingForRomSwap &&
+                !NativeLibrary.isRunning() &&
+                !NativeLibrary.isPaused()
+            ) {
+                if (!DirectoryInitialization.areDirectoriesReady) {
+                    DirectoryInitialization.start()
+                }
 
-        driverViewModel.onLaunchGame()
-    }
+                updateScreenLayout()
 
-    private fun startEmulation(programIndex: Int = 0) {
-        if (!NativeLibrary.isRunning() && !NativeLibrary.isPaused()) {
-            if (!DirectoryInitialization.areDirectoriesReady) {
-                DirectoryInitialization.start()
+                emulationState.run(emulationActivity!!.isActivityRecreated)
             }
-
-            updateScreenLayout()
-
-            emulationState.run(emulationActivity!!.isActivityRecreated, programIndex)
         }
+
+        driverViewModel.onLaunchGame()
     }
 
     override fun onConfigurationChanged(newConfig: Configuration) {
@@ -1375,6 +1396,9 @@ class EmulationFragment : Fragment(), SurfaceHolder.Callback {
         super.onDestroyView()
         amiiboLoadJob?.cancel()
         amiiboLoadJob = null
+        perfStatsRunnable?.let { perfStatsUpdateHandler.removeCallbacks(it) }
+        socRunnable?.let { socUpdateHandler.removeCallbacks(it) }
+        handler.removeCallbacksAndMessages(null)
         clearPausedFrame()
         _binding?.surfaceInputOverlay?.touchEventListener = null
         _binding = null
@@ -1382,7 +1406,9 @@ class EmulationFragment : Fragment(), SurfaceHolder.Callback {
     }
 
     override fun onDetach() {
-        NativeLibrary.clearEmulationActivity()
+        if (!hasNewerEmulationFragment()) {
+            NativeLibrary.clearEmulationActivity()
+        }
         super.onDetach()
     }
 
@@ -1840,10 +1866,74 @@ class EmulationFragment : Fragment(), SurfaceHolder.Callback {
     }
 
     override fun surfaceDestroyed(holder: SurfaceHolder) {
-        emulationState.clearSurface()
+        if (this::emulationState.isInitialized && !hasNewerEmulationFragment()) {
+            emulationState.clearSurface()
+        }
         emulationStarted = false
     }
 
+    private fun hasNewerEmulationFragment(): Boolean {
+        val activity = emulationActivity ?: return false
+        return try {
+            val navHostFragment =
+                activity.supportFragmentManager.findFragmentById(R.id.fragment_container) as? NavHostFragment
+                    ?: return false
+            val currentFragment = navHostFragment.childFragmentManager.fragments
+                .filterIsInstance<EmulationFragment>()
+                .firstOrNull()
+            currentFragment != null && currentFragment !== this
+        } catch (_: Exception) {
+            false
+        }
+    }
+
+    // xbzk: called from EmulationActivity when a new game is loaded while this fragment is still active,
+    // to wait for the emulation thread to stop before allowing the ROM swap to proceed
+    fun notifyWhenEmulationThreadStops(onStopped: () -> Unit) {
+        if (!this::emulationState.isInitialized) {
+            onStopped()
+            return
+        }
+        val emuThread = runCatching { emulationState.emulationThread }.getOrNull()
+        if (emuThread == null || !emuThread.isAlive) {
+            onStopped()
+            return
+        }
+        Thread({
+            runCatching { emuThread.join() }
+            Handler(Looper.getMainLooper()).post {
+                onStopped()
+            }
+        }, "RomSwapWait").start()
+    }
+
+    // xbzk: called from EmulationActivity when a new game is loaded while this
+    // fragment is still active, to stop the current emulation before swapping the ROM
+    fun stopForRomSwap() {
+        if (isStoppingForRomSwap) {
+            return
+        }
+        isStoppingForRomSwap = true
+        clearPausedFrame()
+        emulationViewModel.setIsEmulationStopping(true)
+        _binding?.let {
+            binding.loadingText.setText(R.string.shutting_down)
+            ViewUtils.showView(binding.loadingIndicator)
+            ViewUtils.hideView(binding.inputContainer)
+            ViewUtils.hideView(binding.showStatsOverlayText)
+        }
+        if (this::emulationState.isInitialized) {
+            emulationState.stop()
+            if (NativeLibrary.isRunning() || NativeLibrary.isPaused()) {
+                Log.warning("[EmulationFragment] ROM swap stop fallback: forcing native stop request.")
+                NativeLibrary.stopEmulation()
+            }
+        } else {
+            NativeLibrary.stopEmulation()
+        }
+        NativeConfig.reloadGlobalConfig()
+    }
+
     private fun showOverlayOptions() {
         val anchor = binding.inGameMenu.findViewById<View>(R.id.menu_overlay_controls)
         val popup = PopupMenu(requireContext(), anchor)
@@ -2134,6 +2224,7 @@ class EmulationFragment : Fragment(), SurfaceHolder.Callback {
                 state = State.STOPPED
             } else {
                 Log.warning("[EmulationFragment] Stop called while already stopped.")
+                NativeLibrary.stopEmulation()
             }
         }
 
diff --git a/src/android/app/src/main/java/org/yuzu/yuzu_emu/utils/DirectoryInitialization.kt b/src/android/app/src/main/java/org/yuzu/yuzu_emu/utils/DirectoryInitialization.kt
index f47c60491b..f961c5e984 100644
--- a/src/android/app/src/main/java/org/yuzu/yuzu_emu/utils/DirectoryInitialization.kt
+++ b/src/android/app/src/main/java/org/yuzu/yuzu_emu/utils/DirectoryInitialization.kt
@@ -23,8 +23,8 @@ object DirectoryInitialization {
     fun start() {
         if (!areDirectoriesReady) {
             initializeInternalStorage()
-            NativeLibrary.initializeSystem(false)
             NativeConfig.initializeGlobalConfig()
+            NativeLibrary.initializeSystem(false)
             NativeLibrary.reloadProfiles()
             migrateSettings()
             areDirectoriesReady = true