diff --git a/Makefile.base b/Makefile.base
index ab07fc5c94..00d7eb059d 100644
--- a/Makefile.base
+++ b/Makefile.base
@@ -104,20 +104,30 @@ ASSMOBJ     := $(ASSMSRC:%.S=$(BINDIR)/$(MODULE)/%.o)
 OBJ := $(OBJC) $(OBJCXX) $(ASMOBJ) $(ASSMOBJ) $(GENOBJC)
 DEP := $(OBJC:.o=.d) $(OBJCXX:.o=.d) $(ASSMOBJ:.o=.d)
 
+SRC_ALL := $(SRC) $(SRCXX) $(ASMSRC) $(ASSMSRC)
+SUBDIRS_IN_DIRS := $(filter $(DIRS), $(abspath $(sort $(dir $(SRC_ALL)))))
+ifneq (,$(SUBDIRS_IN_DIRS))
+  $(warning Files of the following subdirectories are selected \
+    both as RIOT modules (using DIRS) and directly as sourcefiles (using SRC): \
+    $(patsubst $(CURDIR)/%,./%, $(SUBDIRS_IN_DIRS)). \
+    Please select a single approach for each subfolder to prevent linking errors.)
+endif
+SUBDIRS := $(filter-out $(BINDIR)/$(MODULE)/, $(dir $(OBJ)))
+
 include $(RIOTMAKE)/blob.inc.mk
 include $(RIOTMAKE)/tools/fixdep.inc.mk
 
-$(BINDIR)/$(MODULE)/:
+$(BINDIR)/$(MODULE)/ $(SUBDIRS):
 	$(Q)mkdir -p $@
 
-OLD_OBJECTS = $(wildcard $(BINDIR)/$(MODULE)/*.o)
+OLD_OBJECTS = $(wildcard $(BINDIR)/$(MODULE)/*.o $(BINDIR)/$(MODULE)/**/*.o)
 
 # do not clean objects from bindist modules
 ifeq (,$(filter $(MODULE),$(BIN_USEMODULE)))
   OBJECTS_TO_REMOVE = $(filter-out $(OBJ),$(OLD_OBJECTS))
 endif
 
-$(MODULE).module compile-commands $(OBJ): | $(BINDIR)/$(MODULE)/
+$(MODULE).module compile-commands $(OBJ): | $(BINDIR)/$(MODULE)/ $(SUBDIRS)
 
 $(MODULE).module: $(OBJ) $(if $(OBJECTS_TO_REMOVE),$(MODULE).cleanup) | $(DIRS:%=ALL--%)
 
diff --git a/Makefile.include b/Makefile.include
index 771f7cfd49..9a5f8292d4 100644
--- a/Makefile.include
+++ b/Makefile.include
@@ -720,6 +720,7 @@ COMPILE_COMMANDS_FLAGS ?= --clangd
 compile-commands: $(COMPILE_COMMANDS_PATH)
 %/compile_commands.json: $(BUILDDEPS)
 	$(Q)DIRS="$(DIRS)" APPLICATION_BLOBS="$(BLOBS)" \
+    APPLICATION_SRC="$(SRC)" APPLICATION_SRCXX="$(SRCXX)" APPLICATION_ASMSRC="$(ASMSRC)" APPLICATION_ASSMSRC="$(ASSMSRC)" \
 	  "$(MAKE)" -C $(APPDIR) -f $(RIOTMAKE)/application.inc.mk compile-commands
 	$(Q)$(RIOTTOOLS)/compile_commands/compile_commands.py $(COMPILE_COMMANDS_FLAGS) $(BINDIR) \
 	  > $@
@@ -744,6 +745,7 @@ $(ELFFILE): $(BASELIBS) $(ARCHIVES) $(LD_SCRIPTS)
 
 $(APPLICATION_MODULE).module: pkg-build $(BUILDDEPS)
 	$(Q)DIRS="$(DIRS)" APPLICATION_BLOBS="$(BLOBS)" \
+    APPLICATION_SRC="$(SRC)" APPLICATION_SRCXX="$(SRCXX)" APPLICATION_ASMSRC="$(ASMSRC)" APPLICATION_ASSMSRC="$(ASSMSRC)" \
 	  "$(MAKE)" -C $(APPDIR) -f $(RIOTMAKE)/application.inc.mk
 $(APPLICATION_MODULE).module: FORCE
 
diff --git a/makefiles/application.inc.mk b/makefiles/application.inc.mk
index 0460b057c1..274ec11445 100644
--- a/makefiles/application.inc.mk
+++ b/makefiles/application.inc.mk
@@ -3,17 +3,20 @@ MODULE = $(APPLICATION_MODULE)
 DIRS += $(RIOTCPU)/$(CPU) $(BOARDDIR)
 DIRS += $(RIOTBASE)/core $(RIOTBASE)/core/lib $(RIOTBASE)/drivers $(RIOTBASE)/sys
 
-# For regular modules, adding files to BLOBS to their Makefile is sufficient to
-# create the corresponding headers.
+# For regular modules, adding files to BLOBS, SRC, SRCXX, ASMSRC or ASSMSRC
+# in their Makefile is sufficient to explicitely set the variables.
 #
 # Application modules are different, as they use this makefile to build, thus
 # application level variables are not available unless exported.
 #
-# But exporting e.g., BLOBS, would pre-set the variable for all
-# submakefiles.
+# But exporting would pre-set the variables for all submakefiles.
 #
-# As workaround, $(RIOTBASE)/Makefile.include passes BLOBS to this
-# Makefile as APPLICATION_BLOBS.
-BLOBS = $(APPLICATION_BLOBS)
+# As workaround, $(RIOTBASE)/Makefile.include passes the above-listed variables
+# to this Makefile as APPLICATION_*.
+BLOBS   = $(APPLICATION_BLOBS)
+SRC     = $(APPLICATION_SRC)
+SRCXX   = $(APPLICATION_SRCXX)
+ASMSRC  = $(APPLICATION_ASMSRC)
+ASSMSRC = $(APPLICATION_ASSMSRC)
 
 include $(RIOTBASE)/Makefile.base