diff --git a/pcsx2-qt/AutoUpdaterDialog.cpp b/pcsx2-qt/AutoUpdaterDialog.cpp
index 10f1ade9ad..32e7a1d7d7 100644
--- a/pcsx2-qt/AutoUpdaterDialog.cpp
+++ b/pcsx2-qt/AutoUpdaterDialog.cpp
@@ -57,7 +57,9 @@
 #define UPDATE_PLATFORM_STR "Linux"
 #endif
 
-#if _M_SSE >= 0x500
+#if MULTI_ISA_SHARED_COMPILATION
+// #undef UPDATE_ADDITIONAL_TAGS
+#elif _M_SSE >= 0x501
 #define UPDATE_ADDITIONAL_TAGS "AVX2"
 #else
 #define UPDATE_ADDITIONAL_TAGS "SSE4"
@@ -208,20 +210,26 @@ void AutoUpdaterDialog::getLatestReleaseComplete(QNetworkReply* reply)
 				const QJsonArray platform_array(assets_object[UPDATE_PLATFORM_STR].toArray());
 				if (!platform_array.isEmpty())
 				{
-					// search for the correct file
+					QJsonObject best_asset;
+					int best_asset_score = 0;
+
+					// search for usable files
 					for (const QJsonValue& asset_value : platform_array)
 					{
 						const QJsonObject asset_object(asset_value.toObject());
 						const QJsonArray additional_tags_array(asset_object["additionalTags"].toArray());
-						bool is_matching_asset = false;
+						bool is_symbols = false;
+						bool is_avx2 = false;
+						bool is_sse4 = false;
 						bool is_qt_asset = false;
+						bool is_perfect_match = false;
 						for (const QJsonValue& additional_tag : additional_tags_array)
 						{
 							const QString additional_tag_str(additional_tag.toString());
 							if (additional_tag_str == QStringLiteral("symbols"))
 							{
 								// we're not interested in symbols downloads
-								is_matching_asset = false;
+								is_symbols = true;
 								break;
 							}
 							else if (additional_tag_str == QStringLiteral("Qt"))
@@ -229,37 +237,57 @@ void AutoUpdaterDialog::getLatestReleaseComplete(QNetworkReply* reply)
 								// found a qt build
 								is_qt_asset = true;
 							}
-
-							// is this the right variant?
+							else if (additional_tag_str == QStringLiteral("SSE4"))
+							{
+								is_sse4 = true;
+							}
+							else if (additional_tag_str == QStringLiteral("AVX2"))
+							{
+								is_avx2 = true;
+							}
+#ifdef UPDATE_ADDITIONAL_TAGS
 							if (additional_tag_str == QStringLiteral(UPDATE_ADDITIONAL_TAGS))
 							{
-								// yep! found the right one. but keep checking in case it's symbols.
-								is_matching_asset = true;
+								// Found the same variant as what's currently running!  But keep checking in case it's symbols.
+								is_perfect_match = true;
 							}
+#endif
 						}
 
-						if (!is_qt_asset || !is_matching_asset)
+						if (!is_qt_asset || is_symbols || (!x86caps.hasAVX2 && is_avx2))
 						{
 							// skip this asset
 							continue;
 						}
 
-						m_latest_version = data_object["version"].toString();
-						m_latest_version_timestamp = QDateTime::fromString(data_object["publishedAt"].toString(), QStringLiteral("yyyy-MM-ddThh:mm:ss.zzzZ"));
-						m_download_url = asset_object["url"].toString();
-						if (!m_latest_version.isEmpty() && !m_download_url.isEmpty())
-						{
-							found_update_info = true;
-							break;
-						}
+						int score;
+						if (is_perfect_match)
+							score = 4; // #1 choice is the one matching this binary
+						else if (is_avx2)
+							score = 3; // Prefer AVX2 over SSE4 (support test was done above)
+						else if (is_sse4)
+							score = 2; // Prefer SSE4 over one with no tags at all
 						else
+							score = 1; // Multi-ISA builds will have no tags, they'll only get picked because they're the only available build
+
+						if (score > best_asset_score)
 						{
-							reportError("missing version/download info");
+							best_asset = std::move(asset_object);
+							best_asset_score = score;
 						}
 					}
 
-					if (!found_update_info)
-						reportError("matching asset not found");
+					if (best_asset_score == 0)
+					{
+						reportError("no matching assets found");
+					}
+					else
+					{
+						m_latest_version = data_object["version"].toString();
+						m_latest_version_timestamp = QDateTime::fromString(data_object["publishedAt"].toString(), QStringLiteral("yyyy-MM-ddThh:mm:ss.zzzZ"));
+						m_download_url = best_asset["url"].toString();
+						found_update_info = true;
+					}
 				}
 				else
 				{
diff --git a/pcsx2/CMakeLists.txt b/pcsx2/CMakeLists.txt
index 65dccd72d8..7968980a8f 100644
--- a/pcsx2/CMakeLists.txt
+++ b/pcsx2/CMakeLists.txt
@@ -999,7 +999,7 @@ set(pcsx2IPUHeaders
 )
 
 if(DISABLE_ADVANCE_SIMD)
-	target_compile_definitions(PCSX2 PRIVATE MULTI_ISA_SHARED_COMPILATION)
+	target_compile_definitions(PCSX2 PUBLIC MULTI_ISA_SHARED_COMPILATION)
 	if(USE_GCC)
 		target_link_options(PCSX2_FLAGS INTERFACE -Wno-odr)
 	endif()
diff --git a/updater/Updater.cpp b/updater/Updater.cpp
index 8c20dada67..8c52356097 100644
--- a/updater/Updater.cpp
+++ b/updater/Updater.cpp
@@ -434,3 +434,19 @@ void Updater::RemoveUpdateZip()
 	if (!FileSystem::DeleteFilePath(m_zip_path.c_str()))
 		m_progress->DisplayFormattedError("Failed to remove update zip '%s'", m_zip_path.c_str());
 }
+
+std::string Updater::FindPCSX2Exe() const
+{
+	for (const FileToUpdate& file : m_update_paths)
+	{
+		const std::string& name = file.destination_filename;
+		if (name.find(FS_OSPATH_SEPARATOR_CHARACTER) != name.npos)
+			continue; // Main exe is expected to be at the top level
+		if (!StringUtil::StartsWithNoCase(name, "pcsx2"))
+			continue;
+		if (!StringUtil::EndsWithNoCase(name, "exe"))
+			continue;
+		return name;
+	}
+	return {};
+}
diff --git a/updater/Updater.h b/updater/Updater.h
index fc5bf31a6c..1e2e28cfa3 100644
--- a/updater/Updater.h
+++ b/updater/Updater.h
@@ -42,6 +42,8 @@ public:
 	void CleanupStagingDirectory();
 	void RemoveUpdateZip();
 
+	std::string FindPCSX2Exe() const;
+
 private:
 	static bool RecursiveDeleteDirectory(const char* path);
 
diff --git a/updater/Windows/WindowsUpdater.cpp b/updater/Windows/WindowsUpdater.cpp
index 92df9eab29..753d3ada8d 100644
--- a/updater/Windows/WindowsUpdater.cpp
+++ b/updater/Windows/WindowsUpdater.cpp
@@ -453,7 +453,7 @@ int WINAPI wWinMain(HINSTANCE hInstance, HINSTANCE hPrevInstance, LPWSTR lpCmdLi
 	const int parent_process_id = StringUtil::FromChars<int>(StringUtil::WideStringToUTF8String(argv[1])).value_or(0);
 	const std::string destination_directory = StringUtil::WideStringToUTF8String(argv[2]);
 	const std::string zip_path = StringUtil::WideStringToUTF8String(argv[3]);
-	const std::wstring program_to_launch(argv[4]);
+	std::wstring program_to_launch(argv[4]);
 	argv.reset();
 
 	if (parent_process_id <= 0 || destination_directory.empty() || zip_path.empty() || program_to_launch.empty())
@@ -493,6 +493,7 @@ int WINAPI wWinMain(HINSTANCE hInstance, HINSTANCE hPrevInstance, LPWSTR lpCmdLi
 		return 1;
 	}
 
+	DeleteFileW(program_to_launch.c_str()); // In case the new exe has a different name, delete the old one to prevent confusion
 	if (!updater.CommitUpdate())
 	{
 		progress.ModalError(
@@ -505,6 +506,21 @@ int WINAPI wWinMain(HINSTANCE hInstance, HINSTANCE hPrevInstance, LPWSTR lpCmdLi
 
 	progress.ModalInformation("Update complete.");
 
+	if (GetFileAttributesW(program_to_launch.c_str()) == INVALID_FILE_ATTRIBUTES)
+	{
+		// New executable doesn't match old, try to find the real one...
+		if (std::string actual_exe = updater.FindPCSX2Exe(); !actual_exe.empty())
+		{
+			std::string full_path = destination_directory + FS_OSPATH_SEPARATOR_STR + actual_exe;
+			program_to_launch = StringUtil::UTF8StringToWideString(full_path);
+		}
+		else
+		{
+			progress.ModalError("Couldn't find PCSX2 in update package, please re-download a fresh version from GitHub.");
+			return 1;
+		}
+	}
+
 	progress.DisplayFormattedInformation("Launching '%s'...",
 		StringUtil::WideStringToUTF8String(program_to_launch).c_str());
 	ShellExecuteW(nullptr, L"open", program_to_launch.c_str(), nullptr, nullptr, SW_SHOWNORMAL);