diff --git a/ports/atmel-samd/Makefile b/ports/atmel-samd/Makefile
index 249f003f9b..62b8065768 100755
--- a/ports/atmel-samd/Makefile
+++ b/ports/atmel-samd/Makefile
@@ -427,6 +427,8 @@ endif
 OBJ += $(addprefix $(BUILD)/, $(SRC_S:.s=.o))
 
 SRC_QSTR += $(SRC_C) $(SRC_SUPERVISOR) $(SRC_COMMON_HAL_EXPANDED) $(SRC_SHARED_MODULE_EXPANDED) $(STM_SRC_C)
+# Sources that only hold QSTRs after pre-processing.
+SRC_QSTR_PREPROCESSOR += peripherals/samd/$(CHIP_FAMILY)/clocks.c
 
 all: $(BUILD)/firmware.bin $(BUILD)/firmware.uf2
 
diff --git a/py/mkrules.mk b/py/mkrules.mk
index 57a51194a8..621d024a96 100644
--- a/py/mkrules.mk
+++ b/py/mkrules.mk
@@ -77,9 +77,9 @@ $(OBJ): | $(HEADER_BUILD)/qstrdefs.generated.h $(HEADER_BUILD)/mpversion.h
 # - if anything in QSTR_GLOBAL_DEPENDENCIES is newer, then process all source files ($^)
 # - else, if list of newer prerequisites ($?) is not empty, then process just these ($?)
 # - else, process all source files ($^) [this covers "make -B" which can set $? to empty]
-$(HEADER_BUILD)/qstr.i.last: $(SRC_QSTR) $(QSTR_GLOBAL_DEPENDENCIES) | $(HEADER_BUILD)/mpversion.h
+$(HEADER_BUILD)/qstr.i.last: $(SRC_QSTR) $(SRC_QSTR_PREPROCESSOR) $(QSTR_GLOBAL_DEPENDENCIES) | $(HEADER_BUILD)/mpversion.h
 	$(ECHO) "GEN $@"
-	$(Q)$(CPP) $(QSTR_GEN_EXTRA_CFLAGS) $(CFLAGS) $(if $(filter $?,$(QSTR_GLOBAL_DEPENDENCIES)),$^,$(if $?,$?,$^)) >$(HEADER_BUILD)/qstr.i.last;
+	$(Q)grep -lE "(MP_QSTR|i18n)" $(if $(filter $?,$(QSTR_GLOBAL_DEPENDENCIES)),$^,$(if $?,$?,$^)) | xargs $(CPP) $(QSTR_GEN_EXTRA_CFLAGS) $(CFLAGS) $(SRC_QSTR_PREPROCESSOR) >$(HEADER_BUILD)/qstr.i.last;
 
 $(HEADER_BUILD)/qstr.split: $(HEADER_BUILD)/qstr.i.last
 	$(STEPECHO) "GEN $@"
@@ -210,4 +210,3 @@ tags:
 	ctags -e -R $(TOP)
 
 -include $(OBJ:.o=.P)
-
diff --git a/py/py.mk b/py/py.mk
index cad8b53ec1..8e1b86a13e 100644
--- a/py/py.mk
+++ b/py/py.mk
@@ -278,7 +278,10 @@ endif
 
 # Sources that may contain qstrings
 SRC_QSTR_IGNORE = py/nlr%
+SRC_QSTR_EMITNATIVE = py/emitn%
 SRC_QSTR = $(SRC_MOD) $(filter-out $(SRC_QSTR_IGNORE),$(PY_CORE_O_BASENAME:.o=.c)) $(PY_EXTMOD_O_BASENAME:.o=.c)
+# Sources that only hold QSTRs after pre-processing.
+SRC_QSTR_PREPROCESSOR = $(addprefix $(TOP)/, $(filter $(SRC_QSTR_EMITNATIVE),$(PY_CORE_O_BASENAME:.o=.c)))
 
 # Anything that depends on FORCE will be considered out-of-date
 FORCE: