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
@@ -1,8 +1,9 @@
 #!/bin/sh
 
-mkdir -p "${NATIVE_BUILD_DIR}"
 cd "${NATIVE_BUILD_DIR}"
-${CMAKE_COMMAND} -G${CMAKE_GENERATOR} "${CMAKE_SOURCE_DIR}" \
+${CMAKE_COMMAND} -G${CMAKE_GENERATOR} \
+    -S "${CMAKE_SOURCE_DIR}" \
+    -B "${NATIVE_BUILD_DIR}" \
     -D__IS_NATIVE_BUILD=1 \
     -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} \
     ${ARGS}