diff --git a/Source/Android/jni/Config/NativeConfig.cpp b/Source/Android/jni/Config/NativeConfig.cpp
index 9681f0ca8e..f8b9397930 100644
--- a/Source/Android/jni/Config/NativeConfig.cpp
+++ b/Source/Android/jni/Config/NativeConfig.cpp
@@ -11,6 +11,7 @@
 #include "Core/ConfigLoaders/GameConfigLoader.h"
 #include "Core/ConfigLoaders/IsSettingSaveable.h"
 #include "jni/AndroidCommon/AndroidCommon.h"
+#include "jni/Host.h"
 
 constexpr jint LAYER_BASE_OR_CURRENT = 0;
 constexpr jint LAYER_BASE = 1;
@@ -122,6 +123,7 @@ Java_org_dolphinemu_dolphinemu_features_settings_model_NativeConfig_loadGameInis
                                                                                  jstring jGameId,
                                                                                  jint jRevision)
 {
+  HostThreadLock guard;
   const std::string game_id = GetJString(env, jGameId);
   const u16 revision = static_cast<u16>(jRevision);
   Config::AddLayer(ConfigLoaders::GenerateGlobalGameConfigLoader(game_id, revision));
@@ -131,6 +133,7 @@ Java_org_dolphinemu_dolphinemu_features_settings_model_NativeConfig_loadGameInis
 JNIEXPORT void JNICALL
 Java_org_dolphinemu_dolphinemu_features_settings_model_NativeConfig_unloadGameInis(JNIEnv*, jclass)
 {
+  HostThreadLock guard;
   Config::RemoveLayer(Config::LayerType::GlobalGame);
   Config::RemoveLayer(Config::LayerType::LocalGame);
 }
@@ -138,6 +141,7 @@ Java_org_dolphinemu_dolphinemu_features_settings_model_NativeConfig_unloadGameIn
 JNIEXPORT void JNICALL Java_org_dolphinemu_dolphinemu_features_settings_model_NativeConfig_save(
     JNIEnv*, jclass, jint layer)
 {
+  HostThreadLock guard;
   return GetLayer(layer, {})->Save();
 }
 
@@ -145,6 +149,7 @@ JNIEXPORT void JNICALL
 Java_org_dolphinemu_dolphinemu_features_settings_model_NativeConfig_deleteAllKeys(JNIEnv*, jclass,
                                                                                   jint layer)
 {
+  HostThreadLock guard;
   return GetLayer(layer, {})->DeleteAllKeys();
 }
 
@@ -161,6 +166,7 @@ JNIEXPORT jboolean JNICALL
 Java_org_dolphinemu_dolphinemu_features_settings_model_NativeConfig_deleteKey(
     JNIEnv* env, jclass, jint layer, jstring file, jstring section, jstring key)
 {
+  HostThreadLock guard;
   const Config::Location location = GetLocation(env, file, section, key);
   const bool had_value = GetLayer(layer, location)->DeleteKey(location);
   if (had_value)
@@ -214,6 +220,7 @@ JNIEXPORT void JNICALL
 Java_org_dolphinemu_dolphinemu_features_settings_model_NativeConfig_setString(
     JNIEnv* env, jclass, jint layer, jstring file, jstring section, jstring key, jstring value)
 {
+  HostThreadLock guard;
   return Set(layer, GetLocation(env, file, section, key), GetJString(env, value));
 }
 
@@ -221,18 +228,21 @@ JNIEXPORT void JNICALL
 Java_org_dolphinemu_dolphinemu_features_settings_model_NativeConfig_setBoolean(
     JNIEnv* env, jclass, jint layer, jstring file, jstring section, jstring key, jboolean value)
 {
+  HostThreadLock guard;
   return Set(layer, GetLocation(env, file, section, key), static_cast<bool>(value));
 }
 
 JNIEXPORT void JNICALL Java_org_dolphinemu_dolphinemu_features_settings_model_NativeConfig_setInt(
     JNIEnv* env, jclass, jint layer, jstring file, jstring section, jstring key, jint value)
 {
+  HostThreadLock guard;
   return Set(layer, GetLocation(env, file, section, key), value);
 }
 
 JNIEXPORT void JNICALL Java_org_dolphinemu_dolphinemu_features_settings_model_NativeConfig_setFloat(
     JNIEnv* env, jclass, jint layer, jstring file, jstring section, jstring key, jfloat value)
 {
+  HostThreadLock guard;
   return Set(layer, GetLocation(env, file, section, key), value);
 }
 }
diff --git a/Source/Android/jni/MainAndroid.cpp b/Source/Android/jni/MainAndroid.cpp
index 0b8a0760ab..90e56822f4 100644
--- a/Source/Android/jni/MainAndroid.cpp
+++ b/Source/Android/jni/MainAndroid.cpp
@@ -489,12 +489,14 @@ JNIEXPORT void JNICALL Java_org_dolphinemu_dolphinemu_NativeLibrary_RefreshWiimo
 
 JNIEXPORT void JNICALL Java_org_dolphinemu_dolphinemu_NativeLibrary_ReloadConfig(JNIEnv*, jclass)
 {
+  HostThreadLock guard;
   SConfig::GetInstance().LoadSettings();
 }
 
 JNIEXPORT void JNICALL
 Java_org_dolphinemu_dolphinemu_NativeLibrary_UpdateGCAdapterScanThread(JNIEnv*, jclass)
 {
+  HostThreadLock guard;
   if (GCAdapter::UseAdapter())
   {
     GCAdapter::StartScanThread();
@@ -507,6 +509,9 @@ Java_org_dolphinemu_dolphinemu_NativeLibrary_UpdateGCAdapterScanThread(JNIEnv*,
 
 JNIEXPORT void JNICALL Java_org_dolphinemu_dolphinemu_NativeLibrary_Initialize(JNIEnv*, jclass)
 {
+  // InitControllers ends up calling config code, and some config callbacks use RunAsCPUThread
+  HostThreadLock guard;
+
   UICommon::CreateDirectories();
   Common::RegisterMsgAlertHandler(&MsgAlert);
   Common::AndroidSetReportHandler(&ReportSend);
@@ -621,6 +626,7 @@ JNIEXPORT void JNICALL Java_org_dolphinemu_dolphinemu_NativeLibrary_RunSystemMen
 JNIEXPORT void JNICALL Java_org_dolphinemu_dolphinemu_NativeLibrary_ChangeDisc(JNIEnv* env, jclass,
                                                                                jstring jFile)
 {
+  HostThreadLock guard;
   const std::string path = GetJString(env, jFile);
   __android_log_print(ANDROID_LOG_INFO, DOLPHIN_TAG, "Change Disc: %s", path.c_str());
   Core::RunAsCPUThread([&path] { Core::System::GetInstance().GetDVDInterface().ChangeDisc(path); });