diff --git a/pkg/micropython/Makefile b/pkg/micropython/Makefile
index 4dd9e1536e..d5fc6f1851 100644
--- a/pkg/micropython/Makefile
+++ b/pkg/micropython/Makefile
@@ -5,8 +5,12 @@ PKG_LICENSE=MIT
 
 CFLAGS += -Wno-implicit-fallthrough -Wno-unused-parameter -Wno-error
 
+# Micropython build system doesn't support (yet) out-of-source builds
+# so clone and build micropython within the application build directory
+PKG_BUILD_OUT_OF_SOURCE = 0
+
 include $(RIOTBASE)/pkg/pkg.mk
 
 all:
-	@mkdir -p $(PKG_BUILDDIR)/tmp
-	BUILD=$(PKG_BUILDDIR) "$(MAKE)" -C $(PKG_BUILDDIR)/ports/riot
+	@mkdir -p $(PKG_BUILD_DIR)/tmp
+	BUILD=$(PKG_BUILD_DIR) "$(MAKE)" -C $(PKG_SOURCE_DIR)/ports/riot
diff --git a/pkg/micropython/Makefile.include b/pkg/micropython/Makefile.include
index b19a7006b7..4b60bb2649 100644
--- a/pkg/micropython/Makefile.include
+++ b/pkg/micropython/Makefile.include
@@ -5,8 +5,8 @@ CFLAGS += -DMP_RIOT_HEAPSIZE=$(MP_RIOT_HEAPSIZE)
 
 # include paths
 INCLUDES += -I$(RIOTBASE)/pkg/micropython/include
-INCLUDES += -I$(PKGDIRBASE)/micropython
-INCLUDES += -I$(PKGDIRBASE)/micropython/ports/riot
+INCLUDES += -I$(BINDIR)/pkg/micropython
+INCLUDES += -I$(BINDIR)/pkg/micropython/ports/riot
 
 # The port currently doesn't build with llvm
 TOOLCHAINS_BLACKLIST += llvm
diff --git a/pkg/nordic_softdevice_ble/Makefile b/pkg/nordic_softdevice_ble/Makefile
index 509589ee48..79f8bd89ca 100644
--- a/pkg/nordic_softdevice_ble/Makefile
+++ b/pkg/nordic_softdevice_ble/Makefile
@@ -5,9 +5,10 @@ PKG_URL = https://developer.nordicsemi.com/nRF5_IoT_SDK/nRF5_IoT_SDK_v0.9.x/$(PK
 PKG_MD5 = 291c875df69c51e22491e6112128bd9c
 PKG_LICENSE = nordic-bsd
 
-PKG_DIR=$(CURDIR)
-PKG_BUILDDIR=$(PKGDIRBASE)/$(PKG_NAME)
-PKG_SRCDIR=$(PKG_BUILDDIR)/src
+PKG_DIR = $(CURDIR)
+PKG_BUILD_DIR = $(BINDIR)/pkg/$(PKG_NAME)
+PKG_SOURCE_DIR = $(PKGDIRBASE)/$(PKG_NAME)
+PKG_SRCDIR  = $(PKG_SOURCE_DIR)/src
 
 SOFTDEVICE := components/softdevice/s1xx_iot/s1xx-iot-prototype3_nrf52_softdevice.hex
 BLE_6LOWPAN_LIB := components/iot/ble_6lowpan/lib/ble_6lowpan.a
@@ -21,13 +22,13 @@ all: $(BINDIR)/ble_6lowpan.a $(BINDIR)/softdevice.hex $(SOFTDEVICE_MODULES)
 prepare: $(PKG_SRCDIR)/.extracted
 
 softdevice_handler:
-	make -C $(PKG_BUILDDIR)/src/components/softdevice/common/softdevice_handler -f $(RIOTBASE)/Makefile.base
+	"$(MAKE)" -C $(PKG_SRCDIR)/components/softdevice/common/softdevice_handler -f $(RIOTBASE)/Makefile.base
 
 ble_common:
-	make -C $(PKG_BUILDDIR)/src/components/ble/common -f $(CURDIR)/ble_common.mk
+	"$(MAKE)" -C $(PKG_SRCDIR)/components/ble/common -f $(CURDIR)/ble_common.mk
 
 ble_ipsp:
-	make -C $(PKG_BUILDDIR)/src/components/iot/ble_ipsp -f $(RIOTBASE)/Makefile.base
+	"$(MAKE)" -C $(PKG_SRCDIR)/components/iot/ble_ipsp -f $(RIOTBASE)/Makefile.base
 
 $(BINDIR)/ble_6lowpan.a: $(PKG_SRCDIR)/.extracted
 	cp $(PKG_SRCDIR)/$(BLE_6LOWPAN_LIB) $@
@@ -38,18 +39,18 @@ $(BINDIR)/ble_6lowpan.a: $(PKG_SRCDIR)/.extracted
 $(BINDIR)/softdevice.hex: $(PKG_SRCDIR)/.extracted
 	$(Q)$(OBJCOPY) $(OFLAGS) -Oihex --gap-fill 0xff $(PKG_SRCDIR)/$(SOFTDEVICE) $@
 
-$(PKG_SRCDIR)/.extracted: $(PKG_BUILDDIR)/$(PKG_FILE)
+$(PKG_SRCDIR)/.extracted: $(PKG_SOURCE_DIR)/$(PKG_FILE)
 	rm -rf $(@D)
 	mkdir -p $(@D)
-	$(Q)cd $(@D) && $(UNZIP_HERE) $(PKG_BUILDDIR)/$(PKG_FILE)
+	$(Q)cd $(@D) && $(UNZIP_HERE) $(PKG_SOURCE_DIR)/$(PKG_FILE)
 	touch $@
 
-$(PKG_BUILDDIR)/$(PKG_FILE):
+$(PKG_SOURCE_DIR)/$(PKG_FILE):
 	@mkdir -p $(@D)
 	$(Q)$(DLCACHE) $(PKG_URL) $(PKG_MD5) $@
 
 clean::
-	rm -rf $(PKG_SRCDIR)/
+	rm -rf $(PKG_SOURCE_DIR)/
 
 distclean::
-	rm -rf $(PKG_BUILDDIR)/
+	rm -rf $(PKG_BUILD_DIR)/
diff --git a/pkg/openthread/Makefile b/pkg/openthread/Makefile
index 1c09a8c1fd..ada040a2f7 100644
--- a/pkg/openthread/Makefile
+++ b/pkg/openthread/Makefile
@@ -3,6 +3,10 @@ PKG_URL=https://github.com/openthread/openthread.git
 PKG_VERSION=thread-reference-20180926
 PKG_LICENSE=BSD-3-Clause
 
+# OpenThread build system doesn't support (yet) out-of-source builds
+# so clone and build OpenThread within the application build directory
+PKG_BUILD_OUT_OF_SOURCE = 0
+
 include $(RIOTBASE)/pkg/pkg.mk
 
 ifneq (,$(filter openthread-ftd,$(USEMODULE)))
@@ -25,7 +29,7 @@ OPENTHREAD_COMMON_FLAGS = -fdata-sections -ffunction-sections -Os
 OPENTHREAD_COMMON_FLAGS += -Wno-implicit-fallthrough -Wno-unused-parameter
 OPENTHREAD_CXXFLAGS += -Wno-class-memaccess
 
-OT_LIB_DIR = $(PKG_BUILDDIR)/output/lib
+OT_LIB_DIR = $(PKG_BUILD_DIR)/output/lib
 MODULE_LIBS = mbedcrypto.a openthread-$(TD).a
 ifneq (,$(filter openthread-cli,$(USEMODULE)))
   MODULE_LIBS += openthread-cli.a
@@ -43,12 +47,12 @@ $(BINDIR)/mbedcrypto.a: $(BINDIR)/openthread-$(TD).a
 $(BINDIR)/openthread-cli.a: $(BINDIR)/openthread-$(TD).a
 	@cp $(OT_LIB_DIR)/libopenthread-cli-$(TD).a $@
 
-$(OT_LIB_DIR)/libopenthread-$(TD).a: $(PKG_BUILDDIR)/Makefile
-	make -C $(PKG_BUILDDIR) -j4 --no-print-directory install DESTDIR=$(PKG_BUILDDIR)/output PREFIX=/
+$(OT_LIB_DIR)/libopenthread-$(TD).a: $(PKG_BUILD_DIR)/Makefile
+	make -C $(PKG_BUILD_DIR) -j4 --no-print-directory install DESTDIR=$(PKG_BUILD_DIR)/output PREFIX=/
 	$(Q)printf "OpenThread built for %s device\n" $(TD)
 
-$(PKG_BUILDDIR)/Makefile: $(PKG_BUILDDIR)/configure
-	$(Q)cd $(PKG_BUILDDIR) && CPP="$(CPP)" CC="$(CC)" CXX="$(CXX)"\
+$(PKG_BUILD_DIR)/Makefile: $(PKG_BUILD_DIR)/configure
+	$(Q)cd $(PKG_BUILD_DIR) && CPP="$(CPP)" CC="$(CC)" CXX="$(CXX)"\
 		OBJC="" OBJCXX="" AR="$(AR)" RANLIB="$(RANLIB)" NM="$(NM)" \
 		STRIP="$(STRIP)" \
 		CPPFLAGS="$(OPENTHREAD_COMMON_FLAGS) $(CFLAGS_CPU) -D$(CONFIG_FILE)" \
@@ -60,6 +64,6 @@ $(PKG_BUILDDIR)/Makefile: $(PKG_BUILDDIR)/configure
 		./configure --disable-docs --host=$(TARGET_ARCH) --target=$(TARGET_ARCH) \
 		--prefix=/ --enable-default-logging $(OPENTHREAD_ARGS)
 
-$(PKG_BUILDDIR)/configure: $(PKG_PREPARED)
+$(PKG_BUILD_DIR)/configure: $(PKG_PREPARED)
 	$(Q)printf "OPENTHREAD_ARGS is [$(OPENTHREAD_ARGS)]\n"
-	$(Q)cd $(PKG_BUILDDIR) && PREFIX="/" ./bootstrap
+	$(Q)cd $(PKG_BUILD_DIR) && PREFIX="/" ./bootstrap
diff --git a/pkg/openthread/Makefile.include b/pkg/openthread/Makefile.include
index 5121661545..e8301970a5 100644
--- a/pkg/openthread/Makefile.include
+++ b/pkg/openthread/Makefile.include
@@ -1,7 +1,7 @@
 OPENTHREAD_DIR = $(RIOTBASE)/pkg/openthread
 
 INCLUDES += -I$(OPENTHREAD_DIR)/include \
-            -I$(PKGDIRBASE)/openthread/include
+            -I$(BINDIR)/pkg/openthread/include
 
 ifneq (,$(filter openthread_contrib,$(USEMODULE)))
   DIRS += $(OPENTHREAD_DIR)/contrib