diff --git a/changes/2532.misc.md b/changes/2532.misc.md
new file mode 100644
index 0000000000..0f04ec6173
--- /dev/null
+++ b/changes/2532.misc.md
@@ -0,0 +1 @@
+The GNOME runtime for Toga Flatpak builds was updated to 49.
diff --git a/src/briefcase/bootstraps/toga.py b/src/briefcase/bootstraps/toga.py
index 671e7aad6a..79021841be 100644
--- a/src/briefcase/bootstraps/toga.py
+++ b/src/briefcase/bootstraps/toga.py
@@ -58,7 +58,9 @@ def pyproject_table_macOS(self):
     def pyproject_table_linux(self):
         return """\
 requires = [
-    "toga-gtk~=0.5.0",
+    "git+https://github.com/beeware/toga@main#subdirectory=core",
+    "git+https://github.com/beeware/toga@main#subdirectory=travertino",
+    "git+https://github.com/beeware/toga@main#subdirectory=gtk",
     # PyGObject 3.52.1 enforces a requirement on libgirepository-2.0-dev. This library
     # isn't available on Debian 12/Ubuntu 22.04. If you don't need to support those (or
     # older) releases, you can remove this version pin. See beeware/toga#3143.
@@ -191,7 +193,7 @@ def pyproject_table_linux_appimage(self):
     def pyproject_table_linux_flatpak(self):
         return """\
 flatpak_runtime = "org.gnome.Platform"
-flatpak_runtime_version = "48"
+flatpak_runtime_version = "50"
 flatpak_sdk = "org.gnome.Sdk"
 """
 
diff --git a/tests/commands/new/test_build_gui_context.py b/tests/commands/new/test_build_gui_context.py
index b2e413f033..799cd6a58b 100644
--- a/tests/commands/new/test_build_gui_context.py
+++ b/tests/commands/new/test_build_gui_context.py
@@ -85,7 +85,9 @@ def main():
 """,
         "pyproject_table_linux": """\
 requires = [
-    "toga-gtk~=0.5.0",
+    "git+https://github.com/beeware/toga@main#subdirectory=core",
+    "git+https://github.com/beeware/toga@main#subdirectory=travertino",
+    "git+https://github.com/beeware/toga@main#subdirectory=gtk",
     # PyGObject 3.52.1 enforces a requirement on libgirepository-2.0-dev. This library
     # isn't available on Debian 12/Ubuntu 22.04. If you don't need to support those (or
     # older) releases, you can remove this version pin. See beeware/toga#3143.
@@ -206,7 +208,7 @@ def main():
 """,
         "pyproject_table_linux_flatpak": """\
 flatpak_runtime = "org.gnome.Platform"
-flatpak_runtime_version = "48"
+flatpak_runtime_version = "50"
 flatpak_sdk = "org.gnome.Sdk"
 """,
         "pyproject_table_windows": """\