diff --git a/builddefs/build_keyboard.mk b/builddefs/build_keyboard.mk
index 32e41e7d5b38..72c990abbba7 100644
--- a/builddefs/build_keyboard.mk
+++ b/builddefs/build_keyboard.mk
@@ -440,10 +440,11 @@ include $(PLATFORM_PATH)/$(PLATFORM_KEY)/platform.mk
 -include $(PLATFORM_PATH)/$(PLATFORM_KEY)/flash.mk
 
 ifneq ($(strip $(PROTOCOL)),)
-    include $(TMK_PATH)/protocol/$(strip $(shell echo $(PROTOCOL) | tr '[:upper:]' '[:lower:]')).mk
+PROTOCOL_KEY = $(strip $(shell echo $(PROTOCOL) | tr '[:upper:]' '[:lower:]'))
 else
-    include $(TMK_PATH)/protocol/$(PLATFORM_KEY).mk
+PROTOCOL_KEY = $(PLATFORM_KEY)
 endif
+include $(TMK_PATH)/protocol/$(PROTOCOL_KEY)/$(PROTOCOL_KEY).mk
 
 # Setup definitions based on the selected MCU
 $(eval $(call add_qmk_prefix_defs,MCU_ORIG,MCU))
diff --git a/tmk_core/protocol.mk b/tmk_core/protocol.mk
index d3f15c458876..2ae7aa9abea5 100644
--- a/tmk_core/protocol.mk
+++ b/tmk_core/protocol.mk
@@ -99,7 +99,7 @@ ifeq ($(strip $(SHARED_EP_ENABLE)), yes)
 endif
 
 ifeq ($(strip $(USB_HID_ENABLE)), yes)
-    include $(TMK_DIR)/protocol/usb_hid.mk
+    include $(TMK_DIR)/protocol/usb_hid/usb_hid.mk
 endif
 
 # Search Path
diff --git a/tmk_core/protocol/arm_atsam.mk b/tmk_core/protocol/arm_atsam/arm_atsam.mk
similarity index 100%
rename from tmk_core/protocol/arm_atsam.mk
rename to tmk_core/protocol/arm_atsam/arm_atsam.mk
diff --git a/tmk_core/protocol/chibios.mk b/tmk_core/protocol/chibios/chibios.mk
similarity index 100%
rename from tmk_core/protocol/chibios.mk
rename to tmk_core/protocol/chibios/chibios.mk
diff --git a/tmk_core/protocol/lufa.mk b/tmk_core/protocol/lufa/lufa.mk
similarity index 100%
rename from tmk_core/protocol/lufa.mk
rename to tmk_core/protocol/lufa/lufa.mk
diff --git a/tmk_core/protocol/usb_hid.mk b/tmk_core/protocol/usb_hid/usb_hid.mk
similarity index 100%
rename from tmk_core/protocol/usb_hid.mk
rename to tmk_core/protocol/usb_hid/usb_hid.mk
diff --git a/tmk_core/protocol/vusb.mk b/tmk_core/protocol/vusb/vusb.mk
similarity index 100%
rename from tmk_core/protocol/vusb.mk
rename to tmk_core/protocol/vusb/vusb.mk