diff --git a/Makefile.base b/Makefile.base
index a0fddf52bc..57fdc4f7fb 100644
--- a/Makefile.base
+++ b/Makefile.base
@@ -107,33 +107,46 @@ $(OBJC_LTO): CFLAGS+=$(LTOFLAGS)
 
 # Define dependencies for object files
 OBJ_DEPS += $(RIOTBUILD_CONFIG_HEADER_C)
-ifneq (,$(SHOULD_RUN_KCONFIG))
-  OBJ_DEPS += $(KCONFIG_GENERATED_AUTOCONF_HEADER_C)
-endif
 
-$(OBJC): $(BINDIR)/$(MODULE)/%.o: %.c $(OBJ_DEPS)
+$(OBJC): $(BINDIR)/$(MODULE)/%.o: %.c $(OBJ_DEPS) | $(if $(SHOULD_RUN_KCONFIG),$(KCONFIG_GENERATED_AUTOCONF_HEADER_C))
 	$(Q)$(CCACHE) $(CC) \
 		-DRIOT_FILE_RELATIVE=\"$(patsubst $(RIOTBASE)/%,%,$(abspath $<))\" \
 		-DRIOT_FILE_NOPATH=\"$(notdir $<)\" \
 		$(CFLAGS) $(INCLUDES) -MQ '$@' -MD -MP -c -o $@ $(abspath $<)
+ifneq (,$(SHOULD_RUN_KCONFIG))
+	$(Q)$(FIXDEP) $(@:.o=.d) $@ $(KCONFIG_SYNC_DIR) > $(@:.o=.tmp)
+	$(Q)mv $(@:.o=.tmp) $(@:.o=.d)
+endif
 
-$(GENOBJC): %.o: %.c $(OBJ_DEPS)
+$(GENOBJC): %.o: %.c $(OBJ_DEPS) | $(if $(SHOULD_RUN_KCONFIG),$(KCONFIG_GENERATED_AUTOCONF_HEADER_C))
 	$(Q) $(CCACHE) $(CC) \
 		-DRIOT_FILE_RELATIVE=\"$(patsubst $(RIOTBASE)/%,%,$<)\" \
 		-DRIOT_FILE_NOPATH=\"$(notdir $<)\" \
 		$(CFLAGS) $(INCLUDES) -MQ '$@' -MD -MP -c -o $@ $<
+ifneq (,$(SHOULD_RUN_KCONFIG))
+	$(Q)$(FIXDEP) $(@:.o=.d) $@ $(KCONFIG_SYNC_DIR) > $(@:.o=.tmp)
+	$(Q)mv $(@:.o=.tmp) $(@:.o=.d)
+endif
 
-$(OBJCXX): $(BINDIR)/$(MODULE)/%.o: %.$(SRCXXEXT) $(OBJ_DEPS)
+$(OBJCXX): $(BINDIR)/$(MODULE)/%.o: %.$(SRCXXEXT) $(OBJ_DEPS) | $(if $(SHOULD_RUN_KCONFIG),$(KCONFIG_GENERATED_AUTOCONF_HEADER_C))
 	$(Q)$(CCACHE) $(CXX) \
 		-DRIOT_FILE_RELATIVE=\"$(patsubst $(RIOTBASE)/%,%,$(abspath $<))\" \
 		-DRIOT_FILE_NOPATH=\"$(notdir $<)\" \
 		$(CXXFLAGS) $(CXXINCLUDES) $(INCLUDES) -MQ '$@' -MD -MP -c -o $@ $(abspath $<)
+ifneq (,$(SHOULD_RUN_KCONFIG))
+	$(Q)$(FIXDEP) $(@:.o=.d) $@ $(KCONFIG_SYNC_DIR) > $(@:.o=.tmp)
+	$(Q)mv $(@:.o=.tmp) $(@:.o=.d)
+endif
 
 $(ASMOBJ): $(BINDIR)/$(MODULE)/%.o: %.s
 	$(Q)$(AS) $(ASFLAGS) -o $@ $(abspath $<)
 
-$(ASSMOBJ): $(BINDIR)/$(MODULE)/%.o: %.S $(OBJ_DEPS)
+$(ASSMOBJ): $(BINDIR)/$(MODULE)/%.o: %.S $(OBJ_DEPS) | $(if $(SHOULD_RUN_KCONFIG),$(KCONFIG_GENERATED_AUTOCONF_HEADER_C))
 	$(Q)$(CCAS) $(CCASFLAGS) $(INCLUDES) -MQ '$@' -MD -MP -c -o $@ $(abspath $<)
+ifneq (,$(SHOULD_RUN_KCONFIG))
+	$(Q)$(FIXDEP) $(@:.o=.d) $@ $(KCONFIG_SYNC_DIR) > $(@:.o=.tmp)
+	$(Q)mv $(@:.o=.tmp) $(@:.o=.d)
+endif
 
 # pull in dependency info for *existing* .o files
 # deleted header files will be silently ignored
diff --git a/makefiles/kconfig.mk b/makefiles/kconfig.mk
index 8224bc4a6c..341ec45a0d 100644
--- a/makefiles/kconfig.mk
+++ b/makefiles/kconfig.mk
@@ -4,11 +4,14 @@ KCONFIG ?= $(RIOTBASE)/Kconfig
 # Include tools targets
 include $(RIOTMAKE)/tools/kconfiglib.inc.mk
 
+# Include fixdep tool
+include $(RIOTMAKE)/tools/fixdep.inc.mk
+
 # Generated dir will contain Kconfig generated configurations
 GENERATED_DIR = $(BINDIR)/generated
 
 # The sync dir will contain a tree of header files that represent Kconfig symbols
-KCONFIG_SYNC_DIR = $(GENERATED_DIR)/deps
+export KCONFIG_SYNC_DIR = $(GENERATED_DIR)/deps
 
 # This file will contain all generated configuration from kconfig
 export KCONFIG_GENERATED_AUTOCONF_HEADER_C = $(GENERATED_DIR)/autoconf.h
@@ -72,13 +75,13 @@ SHOULD_RUN_KCONFIG ?= $(or $(wildcard $(APPDIR)/*.config), \
                            $(if $(CLEAN),,$(wildcard $(KCONFIG_OUT_CONFIG))), \
                            $(filter menuconfig, $(MAKECMDGOALS)))
 
+# export variable to make it visible in other Makefiles
+export SHOULD_RUN_KCONFIG
+
 ifneq (,$(SHOULD_RUN_KCONFIG))
 
-# Flag to enable the --sync-dir feature of Kconfiglib
-KCONFIG_SYNC_DEPS ?=
-
 # Add configuration header to build dependencies
-BUILDDEPS += $(KCONFIG_GENERATED_AUTOCONF_HEADER_C)
+BUILDDEPS += $(KCONFIG_GENERATED_AUTOCONF_HEADER_C) $(FIXDEP)
 
 # Include configuration header when building
 CFLAGS += -imacros '$(KCONFIG_GENERATED_AUTOCONF_HEADER_C)'
@@ -126,12 +129,11 @@ endif # eq (clean, $(MAKECMDGOALS))
 # as KCONFIG_OUT_CONFIG, and is used to inject the configurations during
 # compilation.
 #
-# This will optionally generate the 'dummy' header files needed for incremental
-# builds.
+# This will generate the 'dummy' header files needed for incremental builds.
 $(KCONFIG_GENERATED_AUTOCONF_HEADER_C): $(KCONFIG_OUT_CONFIG)
 	$(Q) $(GENCONFIG) \
 	  --header-path $(KCONFIG_GENERATED_AUTOCONF_HEADER_C) \
-	  $(if $(KCONFIG_SYNC_DEPS),--sync-deps $(KCONFIG_SYNC_DIR)) \
+	  --sync-deps $(KCONFIG_SYNC_DIR) \
 	  --kconfig-filename $(KCONFIG) \
 	  --config-sources $(KCONFIG_OUT_CONFIG) && \
 	  touch $(KCONFIG_GENERATED_AUTOCONF_HEADER_C)