diff --git a/py/mkenv.mk b/py/mkenv.mk
index 49697d4068df2..9217172a3a977 100644
--- a/py/mkenv.mk
+++ b/py/mkenv.mk
@@ -41,7 +41,6 @@ RM = rm
 ECHO = @echo
 CP = cp
 MKDIR = mkdir
-LN = ln
 SED = sed
 PYTHON = python
 
diff --git a/py/mkrules.mk b/py/mkrules.mk
index 0a5b0085690dd..07a250a2f46e2 100644
--- a/py/mkrules.mk
+++ b/py/mkrules.mk
@@ -128,10 +128,6 @@ $(BUILD)/genhdr/cmodules.h: | $(HEADER_BUILD)/mpversion.h
 	@$(ECHO) "GEN $@"
 	$(Q)$(GEN_CMODULES) $(USER_C_MODULES) > $@
 
-# make sure C modules are put in the build directory
-$(BUILD)/cmodules:
-	@$(LN) -sf "$(realpath $(USER_C_MODULES))" $(BUILD)/cmodules
-
 ifneq ($(PROG),)
 # Build a standalone executable (unix does this)
 
diff --git a/py/py.mk b/py/py.mk
index 3b2bc587a5bcc..8616d6b78b5d9 100644
--- a/py/py.mk
+++ b/py/py.mk
@@ -107,8 +107,7 @@ endif
 ifneq ($(USER_C_MODULES),)
 CFLAGS_MOD += -DMICROPY_CMODULES_INCLUDE_H='"genhdr/cmodules.h"'
 include $(USER_C_MODULES)/*/micropython.mk
-SRC_MOD += $(addprefix $(BUILD)/cmodules/, $(SRC_USERMOD))
-$(SRC_MOD) : | $(BUILD)/cmodules
+SRC_MOD += $(addprefix $(USER_C_MODULES)/, $(SRC_USERMOD))
 SRC_QSTR += $(BUILD)/genhdr/cmodules.h
 endif
 
diff --git a/tools/gen-cmodules.py b/tools/gen-cmodules.py
index 524e3c03d3335..83ba36fd6b2ce 100755
--- a/tools/gen-cmodules.py
+++ b/tools/gen-cmodules.py
@@ -6,6 +6,7 @@
 
 import sys
 import os
+import re
 from glob import glob
 
 def update_modules(path):
@@ -13,15 +14,26 @@ def update_modules(path):
     for module in sorted(os.listdir(path)):
         if not os.path.isfile('%s/%s/micropython.mk' % (path, module)):
             continue # not a module
-        modules.append(module)
+
+        defined = False
+        for (root, dirs, files) in os.walk(os.path.join(path, module)):
+            for f in files:
+                with open(os.path.join(root, f), 'r') as modfile:
+                    for line in modfile:
+                        for module in re.findall(r' mp_obj_module_t (\S+?)_(\S+) ', line):
+                            defined = True
+                            modules.append(module)
+
+        if not defined:
+            modules.append((module, 'user_cmodule'))
 
     # Print header file for all external modules.
     print('// Automatically generated by genmodules.py.\n')
     for module in modules:
-        print('extern const struct _mp_obj_module_t %s_user_cmodule;' % module)
+        print('extern const struct _mp_obj_module_t %s_%s;' % module)
     print('\n#define MICROPY_EXTRA_BUILTIN_MODULES \\')
     for module in modules:
-        print('    { MP_ROM_QSTR(MP_QSTR_%s), MP_ROM_PTR(&%s_user_cmodule) }, \\' % (module, module))
+        print('    { MP_ROM_QSTR(MP_QSTR_%s), MP_ROM_PTR(& %s_%s) }, \\' % (module[0], module[0], module[1]))
     print()
 
 if __name__ == '__main__':