diff --git a/CMakeLists.txt b/CMakeLists.txt
index 11bf00be7..a749acd37 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -136,6 +136,7 @@ option(WITH_INSTRUMENTS "Install instruments" ON)
 option(WITH_WAVETABLES "Install wavetables" ON)
 option(SHOW_OPEN_ASSETS_MENU_ENTRY "Show option to open built-in assets directory (on supported platforms)" OFF)
 option(CONSOLE_SUBSYSTEM "Build Furnace with Console subsystem on Windows" OFF)
+option(FLATPAK_WORKAROUNDS "Enable Flatpak-specific workaround for system file picker" OFF)
 if (APPLE)
   option(FORCE_APPLE_BIN "Force enable binary installation to /bin" OFF)
   option(MAKE_BUNDLE "Make a bundle" OFF)
@@ -159,6 +160,10 @@ if (IS_BIG_ENDIAN)
   list(APPEND DEPENDENCIES_DEFINES "TA_BIG_ENDIAN")
 endif()
 
+if (FLATPAK_WORKAROUNDS)
+  list(APPEND DEPENDENCIES_DEFINES "FLATPAK_WORKAROUNDS")
+endif()
+
 set(DEPENDENCIES_COMPILE_OPTIONS "")
 set(DEPENDENCIES_LIBRARIES "")
 set(DEPENDENCIES_LIBRARY_DIRS "")
diff --git a/src/gui/gui.cpp b/src/gui/gui.cpp
index 081dc04d7..c3b35f387 100644
--- a/src/gui/gui.cpp
+++ b/src/gui/gui.cpp
@@ -2855,24 +2855,6 @@ void FurnaceGUI::processDrags(int dragX, int dragY) {
     fileName+=x; \
   }
 
-#define checkExtensionDual(x,y,fallback) \
-  String lowerCase=fileName; \
-  for (char& i: lowerCase) { \
-    if (i>='A' && i<='Z') i+='a'-'A'; \
-  } \
-  if (lowerCase.size()<4 || (lowerCase.rfind(x)!=lowerCase.size()-4 && lowerCase.rfind(y)!=lowerCase.size()-4)) { \
-    fileName+=fallback; \
-  }
-
-#define checkExtensionTriple(x,y,z,fallback) \
-  String lowerCase=fileName; \
-  for (char& i: lowerCase) { \
-    if (i>='A' && i<='Z') i+='a'-'A'; \
-  } \
-  if (lowerCase.size()<4 || (lowerCase.rfind(x)!=lowerCase.size()-4 && lowerCase.rfind(y)!=lowerCase.size()-4 && lowerCase.rfind(z)!=lowerCase.size()-4)) { \
-    fileName+=fallback; \
-  }
-
 #define drawOpMask(m) \
   ImGui::PushFont(patFont); \
   ImGui::PushID("om_" #m); \
@@ -5146,7 +5128,13 @@ bool FurnaceGUI::loop() {
         } else {
           fileName=fileDialog->getFileName()[0];
         }
+#ifdef FLATPAK_WORKAROUNDS
+        // https://github.com/tildearrow/furnace/issues/2096
+        // Flatpak Portals mangling our path hinders us from adding extension
+        if (fileName!="" && !settings.sysFileDialog) {
+#else
         if (fileName!="") {
+#endif
           if (curFileDialog==GUI_FILE_SAVE) {
             checkExtension(".fur");
           }