diff --git a/src/core/file_sys/patch_manager.cpp b/src/core/file_sys/patch_manager.cpp
index d8b04bb343..9a7204a59b 100644
--- a/src/core/file_sys/patch_manager.cpp
+++ b/src/core/file_sys/patch_manager.cpp
@@ -188,16 +188,23 @@ VirtualDir PatchManager::PatchExeFS(VirtualDir exefs) const {
     }
 
     // check for original NAND style
-    // BUT only if we didn't check external provider (to avoid loading wrong update)
-    if (!checked_external && !checked_manual && update_disabled) {
-        if (std::find(disabled.cbegin(), disabled.cend(), "Update") == disabled.cend()) {
+    // Check NAND if: no external updates exist, OR all external updates are disabled
+    if (!checked_external && !checked_manual) {
+        // Check if any NAND-style update is enabled
+        const bool nand_disabled = std::find(disabled.cbegin(), disabled.cend(), "Update (NAND)") != disabled.cend();
+        const bool sdmc_disabled = std::find(disabled.cbegin(), disabled.cend(), "Update (SDMC)") != disabled.cend();
+        const bool generic_disabled = std::find(disabled.cbegin(), disabled.cend(), "Update") != disabled.cend();
+
+        if (!nand_disabled || !sdmc_disabled || !generic_disabled) {
             update_disabled = false;
         }
-        if (std::find(disabled.cbegin(), disabled.cend(), "Update (NAND)") == disabled.cend()) {
-            update_disabled = false;
-        }
-        if (std::find(disabled.cbegin(), disabled.cend(), "Update (SDMC)") == disabled.cend()) {
+    } else if (update_disabled) {
+        const bool nand_disabled = std::find(disabled.cbegin(), disabled.cend(), "Update (NAND)") != disabled.cend();
+        const bool sdmc_disabled = std::find(disabled.cbegin(), disabled.cend(), "Update (SDMC)") != disabled.cend();
+
+        if (!nand_disabled || !sdmc_disabled) {
             update_disabled = false;
+            enabled_version = std::nullopt;
         }
     }
 
@@ -228,7 +235,7 @@ VirtualDir PatchManager::PatchExeFS(VirtualDir exefs) const {
     }
 
     // Fallback to regular content provider - but only if we didn't check external
-    if (update == nullptr && !checked_external && !checked_manual) {
+    if (update == nullptr && !update_disabled) {
         update = content_provider.GetEntry(update_tid, ContentRecordType::Program);
     }
 
@@ -586,15 +593,26 @@ VirtualFile PatchManager::PatchRomFS(const NCA* base_nca, VirtualFile base_romfs
         }
     }
 
-    if (!checked_external && !checked_manual && update_disabled) {
-        if (std::find(disabled.cbegin(), disabled.cend(), "Update") == disabled.cend() ||
-            std::find(disabled.cbegin(), disabled.cend(), "Update (NAND)") == disabled.cend() ||
-            std::find(disabled.cbegin(), disabled.cend(), "Update (SDMC)") == disabled.cend()) {
+    if (!checked_external && !checked_manual) {
+        const bool nand_disabled = std::find(disabled.cbegin(), disabled.cend(), "Update (NAND)") != disabled.cend();
+        const bool sdmc_disabled = std::find(disabled.cbegin(), disabled.cend(), "Update (SDMC)") != disabled.cend();
+        const bool generic_disabled = std::find(disabled.cbegin(), disabled.cend(), "Update") != disabled.cend();
+
+        if (!nand_disabled || !sdmc_disabled || !generic_disabled) {
             update_disabled = false;
         }
         if (!update_disabled && update_raw == nullptr) {
             update_raw = content_provider.GetEntryRaw(update_tid, type);
         }
+    } else if (update_disabled) {
+        const bool nand_disabled = std::find(disabled.cbegin(), disabled.cend(), "Update (NAND)") != disabled.cend();
+        const bool sdmc_disabled = std::find(disabled.cbegin(), disabled.cend(), "Update (SDMC)") != disabled.cend();
+
+        if (!nand_disabled || !sdmc_disabled) {
+            update_disabled = false;
+            enabled_version = std::nullopt;
+            update_raw = content_provider.GetEntryRaw(update_tid, type);
+        }
     }
 
     if (!update_disabled && update_raw != nullptr && base_nca != nullptr) {
diff --git a/src/yuzu/configuration/configure_per_game_addons.cpp b/src/yuzu/configuration/configure_per_game_addons.cpp
index d70c19c99e..a28e490860 100644
--- a/src/yuzu/configuration/configure_per_game_addons.cpp
+++ b/src/yuzu/configuration/configure_per_game_addons.cpp
@@ -169,12 +169,16 @@ void ConfigurePerGameAddons::LoadConfiguration() {
         first_item->setText(name);
         first_item->setCheckable(true);
 
-        if (patch.type == FileSys::PatchType::Update && patch.numeric_version != 0) {
+        const bool is_external_update = patch.type == FileSys::PatchType::Update &&
+                                        patch.source == FileSys::PatchSource::External &&
+                                        patch.numeric_version != 0;
+
+        if (is_external_update) {
             first_item->setData(static_cast<quint32>(patch.numeric_version), Qt::UserRole);
         }
 
         bool patch_disabled = false;
-        if (patch.type == FileSys::PatchType::Update && patch.numeric_version != 0) {
+        if (is_external_update) {
             std::string disabled_key = fmt::format("Update@{}", patch.numeric_version);
             patch_disabled = std::find(disabled.begin(), disabled.end(), disabled_key) != disabled.end();
         } else {