diff --git a/Source/Core/UICommon/UICommon.cpp b/Source/Core/UICommon/UICommon.cpp
index cb857fd3c7..47a012c4f0 100644
--- a/Source/Core/UICommon/UICommon.cpp
+++ b/Source/Core/UICommon/UICommon.cpp
@@ -306,19 +306,45 @@ void SetUserDirectory(std::string custom_path)
       user_path = home_path + DOLPHIN_DATA_DIR DIR_SEP;
     }
 #else
-    // We are on a non-Apple and non-Android POSIX system, there are 4 cases:
-    // 1. GetExeDirectory()/portable.txt exists
+    // We are on a non-Apple and non-Android POSIX system, there are 5 cases:
+    // 1. Running inside flatpak sandbox
+    //    -> Use XDG basedir
+    // 2. GetExeDirectory()/portable.txt exists
     //    -> Use GetExeDirectory()/User
-    // 2. $DOLPHIN_EMU_USERPATH is set
+    // 3. $DOLPHIN_EMU_USERPATH is set
     //    -> Use $DOLPHIN_EMU_USERPATH
-    // 3. ~/.dolphin-emu directory exists
+    // 4. ~/.dolphin-emu directory exists
     //    -> Use ~/.dolphin-emu
-    // 4. Default
+    // 5. Default
     //    -> Use XDG basedir, see
     //    http://standards.freedesktop.org/basedir-spec/basedir-spec-latest.html
     user_path = home_path + "." DOLPHIN_DATA_DIR DIR_SEP;
     std::string exe_path = File::GetExeDirectory();
-    if (File::Exists(exe_path + DIR_SEP "portable.txt"))
+    if (File::Exists(DIR_SEP ".flatpak-info"))
+    {
+      const char* data_home = getenv("XDG_DATA_HOME");
+      std::string data_path =
+          std::string(data_home && data_home[0] == '/' ? data_home :
+                                                         (home_path + ".local" DIR_SEP "share")) +
+          DIR_SEP DOLPHIN_DATA_DIR DIR_SEP;
+
+      const char* config_home = getenv("XDG_CONFIG_HOME");
+      std::string config_path =
+          std::string(config_home && config_home[0] == '/' ? config_home :
+                                                             (home_path + ".config")) +
+          DIR_SEP DOLPHIN_DATA_DIR DIR_SEP;
+
+      const char* cache_home = getenv("XDG_CACHE_HOME");
+      std::string cache_path =
+          std::string(cache_home && cache_home[0] == '/' ? cache_home : (home_path + ".cache")) +
+          DIR_SEP DOLPHIN_DATA_DIR DIR_SEP;
+
+      File::SetUserPath(D_USER_IDX, data_path);
+      File::SetUserPath(D_CONFIG_IDX, config_path);
+      File::SetUserPath(D_CACHE_IDX, cache_path);
+      return;
+    }
+    else if (File::Exists(exe_path + DIR_SEP "portable.txt"))
     {
       user_path = exe_path + DIR_SEP "User" DIR_SEP;
     }