diff --git a/Makefile b/Makefile
index 9713308e74..efc3380c36 100644
--- a/Makefile
+++ b/Makefile
@@ -55,7 +55,7 @@ RETROLAUNCH_OBJ = tools/retrolaunch/main.o \
 	conf/config_file.o \
 	settings.o
 
-HEADERS = $(wildcard */*.h) $(wildcard *.h)
+HEADERS = $(wildcard */*/*.h) $(wildcard */*.h) $(wildcard *.h)
 
 ifeq ($(findstring Haiku,$(OS)),)
    LIBS = -lm
diff --git a/Makefile.win b/Makefile.win
index 384d765c70..eb9f72d508 100644
--- a/Makefile.win
+++ b/Makefile.win
@@ -51,7 +51,7 @@ JOBJ := conf/config_file.o \
 	input/dinput.o \
 	input/winxinput_joypad.o
 
-HEADERS = $(wildcard */*.h) $(wildcard *.h)
+HEADERS = $(wildcard */*/*.h) $(wildcard */*.h) $(wildcard *.h)
 
 CC = gcc
 CXX = g++