diff --git a/ports/zephyr/Makefile b/ports/zephyr/Makefile
index 0d62e5a7a..4fe655284 100644
--- a/ports/zephyr/Makefile
+++ b/ports/zephyr/Makefile
@@ -8,7 +8,6 @@
 # To build a "minimal" configuration, use "make-minimal" wrapper.
 
 BOARD ?= qemu_x86
-CONF_FILE = prj_$(BOARD)_merged.conf
 OUTDIR_PREFIX = $(BOARD)
 
 # Default heap size is 16KB, which is on conservative side, to let
@@ -92,26 +91,23 @@ build/genhdr/qstr.i.last: | $(Z_EXPORTS)
 LIBMICROPYTHON_EXTRA_CMD = -$(RM) -f outdir/$(OUTDIR_PREFIX)/zephyr.lnk
 
 # MicroPython's global clean cleans everything, fast
-CLEAN_EXTRA = outdir libmicropython.a prj_*_merged.conf
+CLEAN_EXTRA = outdir libmicropython.a
 
 # Clean Zephyr things in Zephyr way
 z_clean:
 	$(MAKE) -f Makefile.zephyr BOARD=$(BOARD) clean
 
-# This rule is for prj_$(BOARD)_merged.conf, not $(CONF_FILE), which
-# can be overriden.
-# prj_$(BOARD).conf is optional, that's why it's resolved with $(wildcard)
-# function.
-prj_$(BOARD)_merged.conf: prj_base.conf $(wildcard prj_$(BOARD).conf)
-	$(PYTHON) makeprj.py prj_base.conf prj_$(BOARD).conf $@
-
 test:
 	cd $(TOP)/tests && ./run-tests --target minimal --device "execpty:make -C ../ports/zephyr run BOARD=$(BOARD) QEMU_PTY=1"
 
 cmake: outdir/$(BOARD)/Makefile
 
-outdir/$(BOARD)/Makefile: $(CONF_FILE)
-	mkdir -p outdir/$(BOARD) && cmake -DBOARD=$(BOARD) -DCONF_FILE=$(CONF_FILE) -Boutdir/$(BOARD) -H.
+ifneq ($(CONF_FILE),)
+CMAKE_MOD += -DCONF_FILE=$(CONF_FILE)
+endif
+
+outdir/$(BOARD)/Makefile:
+	mkdir -p outdir/$(BOARD) && cmake -DBOARD=$(BOARD) $(CMAKE_MOD) -Boutdir/$(BOARD) -H.
 
 $(Z_EXPORTS): outdir/$(BOARD)/Makefile
 	make --no-print-directory -C outdir/$(BOARD) outputexports CMAKE_COMMAND=: >$@
diff --git a/ports/zephyr/prj_96b_carbon.conf b/ports/zephyr/boards/96b_carbon.conf
similarity index 100%
rename from ports/zephyr/prj_96b_carbon.conf
rename to ports/zephyr/boards/96b_carbon.conf
diff --git a/ports/zephyr/prj_disco_l475_iot1.conf b/ports/zephyr/boards/disco_l475_iot1.conf
similarity index 100%
rename from ports/zephyr/prj_disco_l475_iot1.conf
rename to ports/zephyr/boards/disco_l475_iot1.conf
diff --git a/ports/zephyr/prj_frdm_k64f.conf b/ports/zephyr/boards/frdm_k64f.conf
similarity index 100%
rename from ports/zephyr/prj_frdm_k64f.conf
rename to ports/zephyr/boards/frdm_k64f.conf
diff --git a/ports/zephyr/prj_frdm_kw41z.conf b/ports/zephyr/boards/frdm_kw41z.conf
similarity index 100%
rename from ports/zephyr/prj_frdm_kw41z.conf
rename to ports/zephyr/boards/frdm_kw41z.conf
diff --git a/ports/zephyr/prj_mimxrt1050_evk.conf b/ports/zephyr/boards/mimxrt1050_evk.conf
similarity index 100%
rename from ports/zephyr/prj_mimxrt1050_evk.conf
rename to ports/zephyr/boards/mimxrt1050_evk.conf
diff --git a/ports/zephyr/prj_qemu_cortex_m3.conf b/ports/zephyr/boards/qemu_cortex_m3.conf
similarity index 100%
rename from ports/zephyr/prj_qemu_cortex_m3.conf
rename to ports/zephyr/boards/qemu_cortex_m3.conf
diff --git a/ports/zephyr/prj_qemu_x86.conf b/ports/zephyr/boards/qemu_x86.conf
similarity index 100%
rename from ports/zephyr/prj_qemu_x86.conf
rename to ports/zephyr/boards/qemu_x86.conf
diff --git a/ports/zephyr/prj_reel_board.conf b/ports/zephyr/boards/reel_board.conf
similarity index 100%
rename from ports/zephyr/prj_reel_board.conf
rename to ports/zephyr/boards/reel_board.conf
diff --git a/ports/zephyr/prj_rv32m1_vega_ri5cy.conf b/ports/zephyr/boards/rv32m1_vega_ri5cy.conf
similarity index 100%
rename from ports/zephyr/prj_rv32m1_vega_ri5cy.conf
rename to ports/zephyr/boards/rv32m1_vega_ri5cy.conf
diff --git a/ports/zephyr/makeprj.py b/ports/zephyr/makeprj.py
deleted file mode 100644
index 239c877cd..000000000
--- a/ports/zephyr/makeprj.py
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env python3
-import sys
-import os
-import hashlib
-
-
-def hash_file(fname):
-    if not os.path.exists(fname):
-        return b""
-    hasher = hashlib.md5()
-    with open(fname, "rb") as f:
-        hasher.update(f.read())
-    return hasher.digest()
-
-
-old_digest = hash_file(sys.argv[3])
-
-with open(sys.argv[3] + ".tmp", "wb") as f:
-    f.write(open(sys.argv[1], "rb").read())
-    if os.path.exists(sys.argv[2]):
-        f.write(open(sys.argv[2], "rb").read())
-
-new_digest = hash_file(sys.argv[3] + ".tmp")
-
-if new_digest != old_digest:
-    print("Replacing")
-    os.rename(sys.argv[3] + ".tmp", sys.argv[3])
-else:
-    os.remove(sys.argv[3] + ".tmp")
diff --git a/ports/zephyr/prj_base.conf b/ports/zephyr/prj.conf
similarity index 100%
rename from ports/zephyr/prj_base.conf
rename to ports/zephyr/prj.conf