diff --git a/src/citra/citra.cpp b/src/citra/citra.cpp
index 54c643d41..9c79baeda 100644
--- a/src/citra/citra.cpp
+++ b/src/citra/citra.cpp
@@ -1,4 +1,4 @@
-// Copyright Citra Emulator Project / Lime3DS Emulator Project
+// Copyright 2014 Citra Emulator Project
 // Licensed under GPLv2 or any later version
 // Refer to the license.txt file included.
 
diff --git a/src/citra_qt/main.cpp b/src/citra_qt/main.cpp
index ad4162384..cdd4040e8 100644
--- a/src/citra_qt/main.cpp
+++ b/src/citra_qt/main.cpp
@@ -1882,8 +1882,7 @@ void GMainWindow::OnGameListCreateShortcut(u64 program_id, const std::string& ga
         shortcut_path =
             QStandardPaths::writableLocation(QStandardPaths::DesktopLocation).toStdString();
     } else if (target == GameListShortcutTarget::Applications) {
-        shortcut_path =
-            QStandardPaths::writableLocation(QStandardPaths::ApplicationsLocation).toStdString();
+        shortcut_path = GetApplicationsDirectory();
     }
 
     // Icon path and title
diff --git a/src/citra_qt/util/util.cpp b/src/citra_qt/util/util.cpp
index 280ea0929..413e94abc 100644
--- a/src/citra_qt/util/util.cpp
+++ b/src/citra_qt/util/util.cpp
@@ -1,11 +1,14 @@
-// Copyright 2015 Citra Emulator Project
+// Copyright Citra Emulator Project / Lime3DS Emulator Project
 // Licensed under GPLv2 or any later version
 // Refer to the license.txt file included.
 
 #include <array>
 #include <cmath>
 #include <QPainter>
+#include <QStandardPaths>
 #include "citra_qt/util/util.h"
+#include "common/common_paths.h"
+#include "common/file_util.h"
 #include "common/logging/log.h"
 #include "core/loader/smdh.h"
 
@@ -160,3 +163,15 @@ bool SaveIconToFile(const std::filesystem::path& icon_path, const QImage& image)
     return false;
 #endif
 }
+
+const std::string GetApplicationsDirectory() {
+// This alternate method is required for Flatpak compatibility as
+// QStandardPaths::ApplicationsLocation returns a path inside the Flatpak data directory instead of
+// $HOME/.local/share
+#if defined(__linux__) || defined(__FreeBSD__)
+    return FileUtil::GetHomeDirectory() + DIR_SEP + ".local" + DIR_SEP + "share" + DIR_SEP +
+           "applications";
+#else
+    return QStandardPaths::writableLocation(QStandardPaths::ApplicationsLocation).toStdString();
+#endif
+}
\ No newline at end of file
diff --git a/src/citra_qt/util/util.h b/src/citra_qt/util/util.h
index 67bd51a90..428d69ffd 100644
--- a/src/citra_qt/util/util.h
+++ b/src/citra_qt/util/util.h
@@ -1,4 +1,4 @@
-// Copyright 2015 Citra Emulator Project
+// Copyright Citra Emulator Project / Lime3DS Emulator Project
 // Licensed under GPLv2 or any later version
 // Refer to the license.txt file included.
 
@@ -36,3 +36,8 @@ QPixmap GetQPixmapFromSMDH(const std::vector<u8>& smdh_data);
  * @return bool If the operation succeeded
  */
 [[nodiscard]] bool SaveIconToFile(const std::filesystem::path& icon_path, const QImage& image);
+
+/**
+ * @return The user’s applications directory
+ */
+[[nodiscard]] const std::string GetApplicationsDirectory();
diff --git a/src/common/file_util.cpp b/src/common/file_util.cpp
index 88fb2e324..e1f3f9809 100644
--- a/src/common/file_util.cpp
+++ b/src/common/file_util.cpp
@@ -1,7 +1,10 @@
-// Copyright 2013 Dolphin Emulator Project / 2014 Citra Emulator Project
+// Copyright Citra Emulator Project / Lime3DS Emulator Project
 // Licensed under GPLv2 or any later version
 // Refer to the license.txt file included.
 
+// Copyright Dolphin Emulator Project
+// Licensed under GPLv2 or any later version
+
 #include <array>
 #include <fstream>
 #include <limits>
@@ -707,8 +710,8 @@ std::string AppDataRoamingDirectory() {
 /**
  * @return The user’s home directory on POSIX systems
  */
-static const std::string& GetHomeDirectory() {
-    static std::string home_path;
+const std::string GetHomeDirectory() {
+    std::string home_path;
     if (home_path.empty()) {
         const char* envvar = getenv("HOME");
         if (envvar) {
diff --git a/src/common/file_util.h b/src/common/file_util.h
index fdacd7a42..4c168b0df 100644
--- a/src/common/file_util.h
+++ b/src/common/file_util.h
@@ -1,7 +1,10 @@
-// Copyright 2013 Dolphin Emulator Project / 2014 Citra Emulator Project
+// Copyright Citra Emulator Project / Lime3DS Emulator Project
 // Licensed under GPLv2 or any later version
 // Refer to the license.txt file included.
 
+// Copyright Dolphin Emulator Project
+// Licensed under GPLv2 or any later version
+
 #pragma once
 
 #include <array>
@@ -204,6 +207,7 @@ void UpdateUserPath(UserPath path, const std::string& filename);
 [[nodiscard]] const std::string& GetExeDirectory();
 [[nodiscard]] std::string AppDataRoamingDirectory();
 #else
+[[nodiscard]] const std::string GetHomeDirectory();
 [[nodiscard]] const std::string GetUserDirectory(const std::string& envvar);
 #endif