diff --git a/cmake/modules/NativeExecutable.cmake b/cmake/modules/NativeExecutable.cmake
--- a/cmake/modules/NativeExecutable.cmake
+++ b/cmake/modules/NativeExecutable.cmake
@@ -105,4 +105,7 @@
 	)
 
 	add_custom_target(native-cmake-build DEPENDS "${NATIVE_BUILD_DIR}/CMakeCache.txt")
+
+	# Add the native directory to the list of file to cleanup.
+	set_property(DIRECTORY "${CMAKE_SOURCE_DIR}" APPEND PROPERTY ADDITIONAL_CLEAN_FILES "${NATIVE_BUILD_DIR}")
 endif()