diff --git a/boards/common/arduino-mkr/Makefile b/boards/common/arduino-mkr/Makefile
index 7c64bc0598..b4202bae82 100644
--- a/boards/common/arduino-mkr/Makefile
+++ b/boards/common/arduino-mkr/Makefile
@@ -1,3 +1,8 @@
 MODULE = boards_common_arduino-mkr
 
+ifneq (,$(filter boards_common_samd21-arduino-bootloader,$(USEMODULE)))
+  # Add the samd21-arduino-bootloader directory to the build
+  DIRS += $(RIOTBOARD)/common/samd21-arduino-bootloader
+endif
+
 include $(RIOTBASE)/Makefile.base
diff --git a/boards/common/arduino-mkr/Makefile.dep b/boards/common/arduino-mkr/Makefile.dep
index c15f2eaf26..e33b5e122e 100644
--- a/boards/common/arduino-mkr/Makefile.dep
+++ b/boards/common/arduino-mkr/Makefile.dep
@@ -2,5 +2,13 @@ ifneq (,$(filter saul_default,$(USEMODULE)))
   USEMODULE += saul_gpio
 endif
 
-# setup the samd21 arduino bootloader related dependencies
-include $(RIOTBOARD)/common/samd21-arduino-bootloader/Makefile.dep
+# use arduino-bootloader only if no other stdio_% other than stdio_cdc_acm
+# is requested
+ifeq (,$(filter-out stdio_cdc_acm,$(filter stdio_%,$(USEMODULE))))
+  USEMODULE += boards_common_samd21-arduino-bootloader
+endif
+
+ifneq (,$(filter boards_common_samd21-arduino-bootloader,$(USEMODULE)))
+  # setup the samd21 arduino bootloader related dependencies
+  include $(RIOTBOARD)/common/samd21-arduino-bootloader/Makefile.dep
+endif
diff --git a/boards/common/samd21-arduino-bootloader/Makefile.dep b/boards/common/samd21-arduino-bootloader/Makefile.dep
index 4edaa81458..d1c9d54246 100644
--- a/boards/common/samd21-arduino-bootloader/Makefile.dep
+++ b/boards/common/samd21-arduino-bootloader/Makefile.dep
@@ -1,10 +1,5 @@
-# Provide stdio over USB by default
-# This is a temporary solution until management of stdio is correctly
-# handled by the build system
-DEFAULT_MODULE += stdio_cdc_acm
-
 # This boards requires support for Arduino bootloader.
 USEMODULE += usb_board_reset
-USEMODULE += boards_common_samd21-arduino-bootloader
+USEMODULE += stdio_cdc_acm
 
 FEATURES_REQUIRED += bootloader_arduino
diff --git a/boards/common/samd21-arduino-bootloader/Makefile.include b/boards/common/samd21-arduino-bootloader/Makefile.include
index cbc6d0fba0..a0ada4f21a 100644
--- a/boards/common/samd21-arduino-bootloader/Makefile.include
+++ b/boards/common/samd21-arduino-bootloader/Makefile.include
@@ -26,6 +26,3 @@ term-delay:
 
 TESTRUNNER_CONNECT_DELAY ?= $(TERM_DELAY)
 $(call target-export-variables,test,TESTRUNNER_CONNECT_DELAY)
-
-# Add the samd21-arduino-bootloader directory to the build
-DIRS += $(RIOTBOARD)/common/samd21-arduino-bootloader
diff --git a/boards/common/samd21-arduino-bootloader/reset.c b/boards/common/samd21-arduino-bootloader/reset.c
index ced63c7953..620f5fbee6 100644
--- a/boards/common/samd21-arduino-bootloader/reset.c
+++ b/boards/common/samd21-arduino-bootloader/reset.c
@@ -19,6 +19,8 @@
  * @}
  */
 
+#ifdef MODULE_BOARDS_COMMON_SAMD21_ARDUINO_BOOTLOADER
+
 #define USB_H_USER_IS_RIOT_INTERNAL
 
 #include "usb_board_reset.h"
@@ -41,3 +43,6 @@ void usb_board_reset_in_bootloader(void)
 
     usb_board_reset_in_application();
 }
+#else
+typedef int dont_be_pedantic;
+#endif /* MODULE_BOARDS_COMMON_SAMD21_ARDUINO_BOOTLOADER */
diff --git a/boards/common/sodaq/Makefile b/boards/common/sodaq/Makefile
index 6792d1f556..8d1038131b 100644
--- a/boards/common/sodaq/Makefile
+++ b/boards/common/sodaq/Makefile
@@ -1,3 +1,8 @@
 MODULE = boards_common_sodaq
 
+ifneq (,$(filter boards_common_samd21-arduino-bootloader,$(USEMODULE)))
+  # Add the samd21-arduino-bootloader directory to the build
+  DIRS += $(RIOTBOARD)/common/samd21-arduino-bootloader
+endif
+
 include $(RIOTBASE)/Makefile.base
diff --git a/boards/common/sodaq/Makefile.dep b/boards/common/sodaq/Makefile.dep
index c15f2eaf26..e33b5e122e 100644
--- a/boards/common/sodaq/Makefile.dep
+++ b/boards/common/sodaq/Makefile.dep
@@ -2,5 +2,13 @@ ifneq (,$(filter saul_default,$(USEMODULE)))
   USEMODULE += saul_gpio
 endif
 
-# setup the samd21 arduino bootloader related dependencies
-include $(RIOTBOARD)/common/samd21-arduino-bootloader/Makefile.dep
+# use arduino-bootloader only if no other stdio_% other than stdio_cdc_acm
+# is requested
+ifeq (,$(filter-out stdio_cdc_acm,$(filter stdio_%,$(USEMODULE))))
+  USEMODULE += boards_common_samd21-arduino-bootloader
+endif
+
+ifneq (,$(filter boards_common_samd21-arduino-bootloader,$(USEMODULE)))
+  # setup the samd21 arduino bootloader related dependencies
+  include $(RIOTBOARD)/common/samd21-arduino-bootloader/Makefile.dep
+endif
diff --git a/boards/feather-m0/Makefile b/boards/feather-m0/Makefile
index f8fcbb53a0..c43a63297c 100644
--- a/boards/feather-m0/Makefile
+++ b/boards/feather-m0/Makefile
@@ -1,3 +1,8 @@
 MODULE = board
 
+ifneq (,$(filter boards_common_samd21-arduino-bootloader,$(USEMODULE)))
+  # Add the samd21-arduino-bootloader directory to the build
+  DIRS += $(RIOTBOARD)/common/samd21-arduino-bootloader
+endif
+
 include $(RIOTBASE)/Makefile.base
diff --git a/boards/feather-m0/Makefile.dep b/boards/feather-m0/Makefile.dep
index c15f2eaf26..e33b5e122e 100644
--- a/boards/feather-m0/Makefile.dep
+++ b/boards/feather-m0/Makefile.dep
@@ -2,5 +2,13 @@ ifneq (,$(filter saul_default,$(USEMODULE)))
   USEMODULE += saul_gpio
 endif
 
-# setup the samd21 arduino bootloader related dependencies
-include $(RIOTBOARD)/common/samd21-arduino-bootloader/Makefile.dep
+# use arduino-bootloader only if no other stdio_% other than stdio_cdc_acm
+# is requested
+ifeq (,$(filter-out stdio_cdc_acm,$(filter stdio_%,$(USEMODULE))))
+  USEMODULE += boards_common_samd21-arduino-bootloader
+endif
+
+ifneq (,$(filter boards_common_samd21-arduino-bootloader,$(USEMODULE)))
+  # setup the samd21 arduino bootloader related dependencies
+  include $(RIOTBOARD)/common/samd21-arduino-bootloader/Makefile.dep
+endif
diff --git a/boards/sodaq-one/Makefile b/boards/sodaq-one/Makefile
index f8fcbb53a0..c43a63297c 100644
--- a/boards/sodaq-one/Makefile
+++ b/boards/sodaq-one/Makefile
@@ -1,3 +1,8 @@
 MODULE = board
 
+ifneq (,$(filter boards_common_samd21-arduino-bootloader,$(USEMODULE)))
+  # Add the samd21-arduino-bootloader directory to the build
+  DIRS += $(RIOTBOARD)/common/samd21-arduino-bootloader
+endif
+
 include $(RIOTBASE)/Makefile.base
diff --git a/boards/sodaq-sara-aff/Makefile b/boards/sodaq-sara-aff/Makefile
index f8fcbb53a0..c43a63297c 100644
--- a/boards/sodaq-sara-aff/Makefile
+++ b/boards/sodaq-sara-aff/Makefile
@@ -1,3 +1,8 @@
 MODULE = board
 
+ifneq (,$(filter boards_common_samd21-arduino-bootloader,$(USEMODULE)))
+  # Add the samd21-arduino-bootloader directory to the build
+  DIRS += $(RIOTBOARD)/common/samd21-arduino-bootloader
+endif
+
 include $(RIOTBASE)/Makefile.base