diff --git a/cmake/modules/CustomCommandWithDepFile.cmake b/cmake/modules/CustomCommandWithDepFile.cmake
new file mode 100644
--- /dev/null
+++ b/cmake/modules/CustomCommandWithDepFile.cmake
@@ -0,0 +1,12 @@
+# Allow to easily create a custom command that uses dep file.
+# depfile are a ninja only feature and a hard fail using other generators.
+
+function(add_custom_command_with_depfile)
+	cmake_parse_arguments("" "" "DEPFILE" "" ${ARGN})
+
+	if(_DEPFILE AND "${CMAKE_GENERATOR}" MATCHES "Ninja")
+		set(_dep_file_arg DEPFILE "${_DEPFILE}")
+	endif()
+
+	add_custom_command(${_UNPARSED_ARGUMENTS} ${_dep_file_arg})
+endfunction()
diff --git a/cmake/modules/NativeExecutable.cmake b/cmake/modules/NativeExecutable.cmake
--- a/cmake/modules/NativeExecutable.cmake
+++ b/cmake/modules/NativeExecutable.cmake
@@ -13,6 +13,10 @@
 # It is imperative that NATIVE_BUILD_DIR be in the cache.
 set(NATIVE_BUILD_DIR "${CMAKE_BINARY_DIR}/native" CACHE PATH "The path of the native build directory" FORCE)
 
+# Only ninja support depfiles and this is a hard error with other generators
+# so we need a nice wrapper to handle this mess.
+include(CustomCommandWithDepFile)
+
 function(add_native_executable NAME)
 	if(__IS_NATIVE_BUILD)
 		add_executable(${NAME} EXCLUDE_FROM_ALL ${ARGN})
@@ -32,17 +36,32 @@
 		if(RELATIVE_PATH)
 			string(PREPEND NATIVE_TARGET "${RELATIVE_PATH}/")
 		endif()
+		if("${CMAKE_GENERATOR}" MATCHES "Ninja")
+			set(TARGET "${NATIVE_TARGET}")
+		else()
+			set(TARGET "${NAME}")
+		endif()
+
 		set(NATIVE_BINARY "${NATIVE_BUILD_DIR}/${NATIVE_TARGET}")
+		set(NATIVE_LINK "${CMAKE_CURRENT_BINARY_DIR}/native-${NAME}")
+
+		configure_file(
+			"${CMAKE_SOURCE_DIR}/cmake/templates/NativeBuildRunner.cmake.in"
+			"${CMAKE_CURRENT_BINARY_DIR}/build_native_${NAME}.sh"
+		)
 
 		# We create a symlink because cmake craps itself if the imported
 		# executable has the same name as the executable itself.
 		# https://cmake.org/pipermail/cmake/2019-May/069480.html
-		add_custom_command(
-			OUTPUT "native-${NAME}"
+		add_custom_command_with_depfile(
+			OUTPUT "${NATIVE_LINK}"
 			COMMENT "Building native ${NATIVE_TARGET}"
-			COMMAND ${CMAKE_COMMAND} --build "${NATIVE_BUILD_DIR}" --target "${NAME}"
-			COMMAND ${CMAKE_COMMAND} -E create_symlink "${NATIVE_BINARY}" "native-${NAME}"
-			DEPENDS native-cmake-build ${ARGN}
+			COMMAND "${CMAKE_CURRENT_BINARY_DIR}/build_native_${NAME}.sh"
+			DEPENDS
+				native-cmake-build
+				"${CMAKE_CURRENT_BINARY_DIR}/build_native_${NAME}.sh"
+				${ARGN}
+			DEPFILE "${NATIVE_LINK}.d"
 			VERBATIM USES_TERMINAL
 		)
 
@@ -51,7 +70,7 @@
 
 		# This obviously cannot depend on a file for some mysterious reasons only
 		# the cmake gods are aware of, so we need a phony custom target.
-		add_custom_target("build-native-${NAME}" DEPENDS "native-${NAME}")
+		add_custom_target("build-native-${NAME}" DEPENDS "${NATIVE_LINK}")
 		add_dependencies(${NAME} "build-native-${NAME}")
 	endif()
 endfunction(add_native_executable)
@@ -96,17 +115,13 @@
 	# Set a hook to execute when everything is set.
 	variable_watch(CMAKE_CURRENT_LIST_DIR _gen_native_cmake_hook)
 
-	if("${CMAKE_GENERATOR}" MATCHES "Ninja")
-		set(cmake_cache_dep_file DEPFILE "${NATIVE_BUILD_DIR}/CMakeFiles/CMakeCache.txt.d")
-	endif()
-
-	add_custom_command(
+	add_custom_command_with_depfile(
 		OUTPUT "${NATIVE_BUILD_DIR}/CMakeCache.txt"
 		COMMENT "Preparing native build..."
 		COMMAND "${CMAKE_BINARY_DIR}/config/run_native_cmake.sh"
 		DEPENDS "${CMAKE_BINARY_DIR}/config/run_native_cmake.sh"
 		WORKING_DIRECTORY "${CMAKE_BINARY_DIR}"
-		${cmake_cache_dep_file}
+		DEPFILE "${NATIVE_BUILD_DIR}/CMakeFiles/CMakeCache.txt.d"
 		VERBATIM USES_TERMINAL
 	)
 
diff --git a/cmake/templates/NativeBuildRunner.cmake.in b/cmake/templates/NativeBuildRunner.cmake.in
new file mode 100755
--- /dev/null
+++ b/cmake/templates/NativeBuildRunner.cmake.in
@@ -0,0 +1,14 @@
+#!/bin/sh
+
+cd "${NATIVE_BUILD_DIR}"
+"${CMAKE_COMMAND}" --build "${NATIVE_BUILD_DIR}" --target "${TARGET}"
+"${CMAKE_COMMAND}" -E create_symlink "${NATIVE_BINARY}" "${NATIVE_LINK}"
+
+# Ok let's generate a depfile if we can.
+if test "x${CMAKE_GENERATOR}" = "xNinja"; then
+    "${CMAKE_SOURCE_DIR}/cmake/utils/gen-ninja-deps.py" \
+        --build-dir "${NATIVE_BUILD_DIR}" \
+        --base-dir "${CMAKE_BINARY_DIR}" \
+        --ninja "${CMAKE_MAKE_PROGRAM}" \
+        "${RELATIVE_PATH}/native-${NAME}" "${TARGET}" > "${NATIVE_LINK}.d"
+fi
diff --git a/cmake/templates/NativeCmakeRunner.cmake.in b/cmake/templates/NativeCmakeRunner.cmake.in
--- a/cmake/templates/NativeCmakeRunner.cmake.in
+++ b/cmake/templates/NativeCmakeRunner.cmake.in
@@ -9,11 +9,11 @@
 
 # Ok let's generate a depfile if we can.
 if test "x${CMAKE_GENERATOR}" = "xNinja"; then
-	"${CMAKE_SOURCE_DIR}/cmake/utils/gen-ninja-deps.py" \
-	    --build-dir "${NATIVE_BUILD_DIR}" \
-	    --base-dir "${CMAKE_BINARY_DIR}" \
-	    --ninja "${CMAKE_MAKE_PROGRAM}" \
-	    native/CMakeCache.txt build.ninja \
-	    --extra-deps build.ninja \
-	        > "${NATIVE_BUILD_DIR}/CMakeFiles/CMakeCache.txt.d"
+    "${CMAKE_SOURCE_DIR}/cmake/utils/gen-ninja-deps.py" \
+        --build-dir "${NATIVE_BUILD_DIR}" \
+        --base-dir "${CMAKE_BINARY_DIR}" \
+        --ninja "${CMAKE_MAKE_PROGRAM}" \
+        native/CMakeCache.txt build.ninja \
+        --extra-deps build.ninja \
+            > "${NATIVE_BUILD_DIR}/CMakeFiles/CMakeCache.txt.d"
 fi
diff --git a/cmake/utils/gen-ninja-deps.py b/cmake/utils/gen-ninja-deps.py
--- a/cmake/utils/gen-ninja-deps.py
+++ b/cmake/utils/gen-ninja-deps.py
@@ -171,7 +171,7 @@
 
 
 # Collapse everything under the base target.
-basedeps = set(d.encode() for d in extra_deps)
+basedeps = set() if extra_deps is None else set(d.encode() for d in extra_deps)
 for d in deps.values():
     basedeps.update(d)