diff --git a/pyodide_build/tools/cmake/Modules/Platform/Emscripten.cmake b/pyodide_build/tools/cmake/Modules/Platform/Emscripten.cmake
index 78b4487e..f82c8e02 100644
--- a/pyodide_build/tools/cmake/Modules/Platform/Emscripten.cmake
+++ b/pyodide_build/tools/cmake/Modules/Platform/Emscripten.cmake
@@ -102,8 +102,8 @@ endif()
 
 # Set SIDE_MODULE_CFLAGS and SIDE_MODULE_LDFLAGS automatically
 # This is automatically set for Python project, but we often omit these in libraries.
-set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} $ENV{SIDE_MODULE_CFLAGS}")
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} $ENV{SIDE_MODULE_CXXFLAGS}")
+set(CMAKE_C_FLAGS_INIT "${CMAKE_C_FLAGS_INIT} $ENV{SIDE_MODULE_CFLAGS}")
+set(CMAKE_CXX_FLAGS_INIT "${CMAKE_CXX_FLAGS_INIT} $ENV{SIDE_MODULE_CXXFLAGS}")
 set(CMAKE_SHARED_LINKER_FLAGS_INIT "${CMAKE_SHARED_LINKER_FLAGS_INIT} $ENV{SIDE_MODULE_LDFLAGS}")
 set(CMAKE_MODULE_LINKER_FLAGS_INIT "${CMAKE_MODULE_LINKER_FLAGS_INIT} $ENV{SIDE_MODULE_LDFLAGS}")