diff --git a/CMakeLists.txt b/CMakeLists.txt
index 636d5473e3..3495e3b2b3 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -585,7 +585,7 @@ if(UNIX)
 endif()
 
 if(ENABLE_SDL)
-  dolphin_find_optional_system_library(SDL2 Externals/SDL 2.30.6)
+  dolphin_find_optional_system_library(SDL2 Externals/SDL 2.30.9)
 endif()
 
 if(ENABLE_ANALYTICS)
diff --git a/Externals/SDL/CMakeLists.txt b/Externals/SDL/CMakeLists.txt
index c30d8ae979..185f1ed930 100644
--- a/Externals/SDL/CMakeLists.txt
+++ b/Externals/SDL/CMakeLists.txt
@@ -9,7 +9,7 @@ option(SDL_TEST "Build the SDL2_test library" OFF)
 option(SDL_TEST_ENABLED_BY_DEFAULT "" OFF)
 
 # SDL fails to clean up old headers after version upgrades, so do that manually
-set(EXPECTED_SDL_REVISION "SDL-release-2.30.6-0")
+set(EXPECTED_SDL_REVISION "SDL-release-2.30.9-0")
 if (EXISTS "${CMAKE_CURRENT_BINARY_DIR}/SDL/include/SDL2/SDL_revision.h")
   file(READ "${CMAKE_CURRENT_BINARY_DIR}/SDL/include/SDL2/SDL_revision.h" ACTUAL_SDL_REVISION)
   if (NOT "${ACTUAL_SDL_REVISION}" MATCHES "${EXPECTED_SDL_REVISION}")
diff --git a/Externals/SDL/SDL b/Externals/SDL/SDL
index ba2f78a006..c98c4fbff6 160000
--- a/Externals/SDL/SDL
+++ b/Externals/SDL/SDL
@@ -1 +1 @@
-Subproject commit ba2f78a0069118a6c583f1fbf1420144ffa35bad
+Subproject commit c98c4fbff6d8f3016a3ce6685bf8f43433c3efcc
diff --git a/Flatpak/SDL2/SDL2.json b/Flatpak/SDL2/SDL2.json
new file mode 100644
index 0000000000..4c1821b742
--- /dev/null
+++ b/Flatpak/SDL2/SDL2.json
@@ -0,0 +1,21 @@
+{
+  "name": "SDL2",
+  "buildsystem": "autotools",
+  "config-opts": ["--disable-static"],
+  "sources": [
+    {
+      "type": "dir",
+      "path": "../../Externals/SDL/SDL"
+    }
+  ],
+  "cleanup": [ "/bin/sdl2-config",
+               "/include",
+               "/lib/libSDL2.la",
+               "/lib/libSDL2main.a",
+               "/lib/libSDL2main.la",
+               "/lib/libSDL2_test.a",
+               "/lib/libSDL2_test.la",
+               "/lib/cmake",
+               "/share/aclocal",
+               "/lib/pkgconfig"]
+}
diff --git a/Flatpak/org.DolphinEmu.dolphin-emu.yml b/Flatpak/org.DolphinEmu.dolphin-emu.yml
index 7afef2504d..a1266b5df5 100644
--- a/Flatpak/org.DolphinEmu.dolphin-emu.yml
+++ b/Flatpak/org.DolphinEmu.dolphin-emu.yml
@@ -47,6 +47,9 @@ modules:
         url: https://github.com/Unrud/xdg-screensaver-shim/archive/0.0.2.tar.gz
         sha256: 0ed2a69fe6ee6cbffd2fe16f85116db737f17fb1e79bfb812d893cf15c728399
 
+  # build the vendored SDL2 from Externals until the runtime gets 2.30.9
+  - SDL2/SDL2.json
+
   - name: dolphin-emu
     buildsystem: cmake-ninja
     config-opts: