diff --git a/Makefile b/Makefile
index fd5a412b..0e70d5dc 100644
--- a/Makefile
+++ b/Makefile
@@ -1,5 +1,5 @@
 BOARD ?= qemu_x86
-CONF_FILE = zephyr/prj.conf
-SOURCE_DIR = zephyr/src
+CONF_FILE = boot/zephyr/prj.conf
+SOURCE_DIR = boot/zephyr
 
 include ${ZEPHYR_BASE}/Makefile.inc
diff --git a/zephyr/src/Makefile b/boot/zephyr/Makefile
similarity index 60%
rename from zephyr/src/Makefile
rename to boot/zephyr/Makefile
index 0996747c..6b8618ac 100644
--- a/zephyr/src/Makefile
+++ b/boot/zephyr/Makefile
@@ -1,8 +1,8 @@
 subdir-ccflags-y += -I$(PROJECT)/boot/bootutil/include
-subdir-ccflags-y += -I$(PROJECT)/zephyr/include
+subdir-ccflags-y += -I$(PROJECT)/boot/zephyr/include
 
 obj-y += main.o
 obj-y += flash_map.o hal_flash.o os.o
 obj-y += keys.o
 
-obj-y += ../../boot/bootutil/src/
+obj-y += ../bootutil/src/
diff --git a/zephyr/src/flash_map.c b/boot/zephyr/flash_map.c
similarity index 100%
rename from zephyr/src/flash_map.c
rename to boot/zephyr/flash_map.c
diff --git a/zephyr/src/hal_flash.c b/boot/zephyr/hal_flash.c
similarity index 100%
rename from zephyr/src/hal_flash.c
rename to boot/zephyr/hal_flash.c
diff --git a/zephyr/include/flash_map/flash_map.h b/boot/zephyr/include/flash_map/flash_map.h
similarity index 100%
rename from zephyr/include/flash_map/flash_map.h
rename to boot/zephyr/include/flash_map/flash_map.h
diff --git a/zephyr/include/hal/hal_bsp.h b/boot/zephyr/include/hal/hal_bsp.h
similarity index 100%
rename from zephyr/include/hal/hal_bsp.h
rename to boot/zephyr/include/hal/hal_bsp.h
diff --git a/zephyr/include/hal/hal_flash.h b/boot/zephyr/include/hal/hal_flash.h
similarity index 100%
rename from zephyr/include/hal/hal_flash.h
rename to boot/zephyr/include/hal/hal_flash.h
diff --git a/zephyr/include/os/os.h b/boot/zephyr/include/os/os.h
similarity index 100%
rename from zephyr/include/os/os.h
rename to boot/zephyr/include/os/os.h
diff --git a/zephyr/include/os/os_heap.h b/boot/zephyr/include/os/os_heap.h
similarity index 100%
rename from zephyr/include/os/os_heap.h
rename to boot/zephyr/include/os/os_heap.h
diff --git a/zephyr/include/os/os_malloc.h b/boot/zephyr/include/os/os_malloc.h
similarity index 100%
rename from zephyr/include/os/os_malloc.h
rename to boot/zephyr/include/os/os_malloc.h
diff --git a/zephyr/include/syscfg/syscfg.h b/boot/zephyr/include/syscfg/syscfg.h
similarity index 100%
rename from zephyr/include/syscfg/syscfg.h
rename to boot/zephyr/include/syscfg/syscfg.h
diff --git a/zephyr/include/sysflash/sysflash.h b/boot/zephyr/include/sysflash/sysflash.h
similarity index 100%
rename from zephyr/include/sysflash/sysflash.h
rename to boot/zephyr/include/sysflash/sysflash.h
diff --git a/zephyr/src/keys.c b/boot/zephyr/keys.c
similarity index 100%
rename from zephyr/src/keys.c
rename to boot/zephyr/keys.c
diff --git a/zephyr/src/main.c b/boot/zephyr/main.c
similarity index 100%
rename from zephyr/src/main.c
rename to boot/zephyr/main.c
diff --git a/zephyr/src/os.c b/boot/zephyr/os.c
similarity index 100%
rename from zephyr/src/os.c
rename to boot/zephyr/os.c
diff --git a/zephyr/prj.conf b/boot/zephyr/prj.conf
similarity index 100%
rename from zephyr/prj.conf
rename to boot/zephyr/prj.conf
diff --git a/zephyr/target.sh.example b/boot/zephyr/target.sh.example
similarity index 100%
rename from zephyr/target.sh.example
rename to boot/zephyr/target.sh.example