diff --git a/Tools/ardupilotwaf/ardupilotwaf.py b/Tools/ardupilotwaf/ardupilotwaf.py
index ebef10c695..7672c04f41 100644
--- a/Tools/ardupilotwaf/ardupilotwaf.py
+++ b/Tools/ardupilotwaf/ardupilotwaf.py
@@ -247,7 +247,6 @@ def ap_program(bld,
     if use_legacy_defines:
         kw['defines'].extend(get_legacy_defines(bld.path.name))
 
-    kw['cxxflags'] = kw.get('cxxflags', []) + ['-include', 'ap_config.h']
     kw['features'] = kw.get('features', []) + bld.env.AP_PROGRAM_FEATURES
 
     program_groups = Utils.to_list(program_groups)
diff --git a/wscript b/wscript
index 7812ed6f58..0f92a04ddc 100644
--- a/wscript
+++ b/wscript
@@ -364,6 +364,9 @@ def configure(cfg):
 
     cfg.write_config_header(os.path.join(cfg.variant, 'ap_config.h'))
 
+    # add in generated flags
+    cfg.env.CXXFLAGS += ['-include', 'ap_config.h']
+
     _collect_autoconfig_files(cfg)
 
 def collect_dirs_to_recurse(bld, globs, **kw):