diff --git a/Makefile b/Makefile
index 91ab9e4e8..de0a2d415 100644
--- a/Makefile
+++ b/Makefile
@@ -29,6 +29,13 @@ $(info QMK Firmware $(QMK_VERSION))
 endif
 endif
 
+# Determine which qmk cli to use
+ifeq (, $(shell which qmk))
+    QMK_BIN = bin/qmk
+else
+    QMK_BIN = qmk
+endif
+
 # avoid 'Entering|Leaving directory' messages
 MAKEFLAGS += --no-print-directory
 
@@ -501,8 +508,8 @@ endef
 %:
 	# Check if we have the CMP tool installed
 	cmp $(ROOT_DIR)/Makefile $(ROOT_DIR)/Makefile >/dev/null 2>&1; if [ $$? -gt 0 ]; then printf "$(MSG_NO_CMP)"; exit 1; fi;
-	# Ensure that bin/qmk works.
-	if ! bin/qmk hello 1> /dev/null 2>&1; then printf "$(MSG_PYTHON_MISSING)"; exit 1; fi
+	# Ensure that $(QMK_BIN) works.
+	if ! $(QMK_BIN) hello 1> /dev/null 2>&1; then printf "$(MSG_PYTHON_MISSING)"; exit 1; fi
 	# Check if the submodules are dirty, and display a warning if they are
 ifndef SKIP_GIT
 	if [ ! -e lib/chibios ]; then git submodule sync lib/chibios && git submodule update --depth 50 --init lib/chibios; fi
diff --git a/bin/qmk b/bin/qmk
index a3c1be328..28486026f 100755
--- a/bin/qmk
+++ b/bin/qmk
@@ -75,6 +75,8 @@ def main():
     os.environ['ORIG_CWD'] = os.getcwd()
     os.chdir(qmk_dir)
 
+    print('Warning: The bin/qmk script is being deprecated. Please install the QMK CLI: python3 -m pip install qmk', file=sys.stderr)
+
     # Import the subcommands
     import qmk.cli  # noqa
 
diff --git a/build_json.mk b/build_json.mk
index 6e2f9c4c8..8822be6a1 100644
--- a/build_json.mk
+++ b/build_json.mk
@@ -28,4 +28,4 @@ endif
 
 # Generate the keymap.c
 $(KEYBOARD_OUTPUT)/src/keymap.c: $(KEYMAP_JSON)
-	bin/qmk json2c --quiet --output $(KEYMAP_C) $(KEYMAP_JSON)
+	$(QMK_BIN) json2c --quiet --output $(KEYMAP_C) $(KEYMAP_JSON)
diff --git a/build_keyboard.mk b/build_keyboard.mk
index 366d1f5d2..74046a094 100644
--- a/build_keyboard.mk
+++ b/build_keyboard.mk
@@ -12,6 +12,9 @@ endif
 
 include common.mk
 
+# Set the qmk cli to use
+QMK_BIN ?= qmk
+
 # Set the filename for the final firmware binary
 KEYBOARD_FILESAFE := $(subst /,_,$(KEYBOARD))
 TARGET ?= $(KEYBOARD_FILESAFE)_$(KEYMAP)
@@ -97,7 +100,7 @@ MAIN_KEYMAP_PATH_4 := $(KEYBOARD_PATH_4)/keymaps/$(KEYMAP)
 MAIN_KEYMAP_PATH_5 := $(KEYBOARD_PATH_5)/keymaps/$(KEYMAP)
 
 # Pull in rules from info.json
-INFO_RULES_MK = $(shell bin/qmk generate-rules-mk --quiet --escape --keyboard $(KEYBOARD) --output $(KEYBOARD_OUTPUT)/src/rules.mk)
+INFO_RULES_MK = $(shell $(QMK_BIN) generate-rules-mk --quiet --escape --keyboard $(KEYBOARD) --output $(KEYBOARD_OUTPUT)/src/rules.mk)
 include $(INFO_RULES_MK)
 
 # Check for keymap.json first, so we can regenerate keymap.c
@@ -294,10 +297,10 @@ endif
 CONFIG_H += $(KEYBOARD_OUTPUT)/src/info_config.h $(KEYBOARD_OUTPUT)/src/layouts.h
 
 $(KEYBOARD_OUTPUT)/src/info_config.h: $(INFO_JSON_FILES)
-	bin/qmk generate-config-h --quiet --keyboard $(KEYBOARD) --output $(KEYBOARD_OUTPUT)/src/info_config.h
+	$(QMK_BIN) generate-config-h --quiet --keyboard $(KEYBOARD) --output $(KEYBOARD_OUTPUT)/src/info_config.h
 
 $(KEYBOARD_OUTPUT)/src/layouts.h: $(INFO_JSON_FILES)
-	bin/qmk generate-layouts --quiet --keyboard $(KEYBOARD) --output $(KEYBOARD_OUTPUT)/src/layouts.h
+	$(QMK_BIN) generate-layouts --quiet --keyboard $(KEYBOARD) --output $(KEYBOARD_OUTPUT)/src/layouts.h
 
 generated-files: $(KEYBOARD_OUTPUT)/src/info_config.h $(KEYBOARD_OUTPUT)/src/layouts.h
 
diff --git a/lib/python/qmk/commands.py b/lib/python/qmk/commands.py
index 3c6f0d001..233d1034b 100644
--- a/lib/python/qmk/commands.py
+++ b/lib/python/qmk/commands.py
@@ -180,6 +180,7 @@ def compile_configurator_json(user_keymap, bootloader=None, parallel=1, **env_va
         f'VERBOSE={verbose}',
         f'COLOR={color}',
         'SILENT=false',
+        'QMK_BIN=qmk',
     ])
 
     return make_command
diff --git a/lib/python/qmk/tests/test_cli_commands.py b/lib/python/qmk/tests/test_cli_commands.py
index 82c42a20e..bfecebdd7 100644
--- a/lib/python/qmk/tests/test_cli_commands.py
+++ b/lib/python/qmk/tests/test_cli_commands.py
@@ -8,7 +8,7 @@ is_windows = 'windows' in platform.platform().lower()
 
 
 def check_subcommand(command, *args):
-    cmd = ['bin/qmk', command, *args]
+    cmd = ['qmk', command, *args]
     result = run(cmd, stdout=PIPE, stderr=STDOUT, universal_newlines=True)
     return result
 
@@ -17,7 +17,7 @@ def check_subcommand_stdin(file_to_read, command, *args):
     """Pipe content of a file to a command and return output.
     """
     with open(file_to_read, encoding='utf-8') as my_file:
-        cmd = ['bin/qmk', command, *args]
+        cmd = ['qmk', command, *args]
         result = run(cmd, stdin=my_file, stdout=PIPE, stderr=STDOUT, universal_newlines=True)
     return result