diff --git a/lib/python/qmk/cli/doctor/main.py b/lib/python/qmk/cli/doctor/main.py
index 5e93fad36..6a31ccdfd 100755
--- a/lib/python/qmk/cli/doctor/main.py
+++ b/lib/python/qmk/cli/doctor/main.py
@@ -9,8 +9,9 @@ from milc import cli
 from milc.questions import yesno
 
 from qmk import submodules
-from qmk.constants import QMK_FIRMWARE
-from .check import CheckStatus, check_binaries, check_binary_versions, check_submodules, check_git_repo
+from qmk.constants import QMK_FIRMWARE, QMK_FIRMWARE_UPSTREAM
+from .check import CheckStatus, check_binaries, check_binary_versions, check_submodules
+from qmk.commands import git_check_repo, git_get_branch, git_is_dirty, git_get_remotes, git_check_deviation, in_virtualenv
 
 
 def os_tests():
@@ -32,6 +33,37 @@ def os_tests():
         return CheckStatus.WARNING
 
 
+def git_tests():
+    """Run Git-related checks
+    """
+    status = CheckStatus.OK
+
+    # Make sure our QMK home is a Git repo
+    git_ok = git_check_repo()
+    if not git_ok:
+        cli.log.warning("{fg_yellow}QMK home does not appear to be a Git repository! (no .git folder)")
+        status = CheckStatus.WARNING
+    else:
+        git_branch = git_get_branch()
+        if git_branch:
+            cli.log.info('Git branch: %s', git_branch)
+            git_dirty = git_is_dirty()
+            if git_dirty:
+                cli.log.warning('{fg_yellow}Git has unstashed/uncommitted changes.')
+                status = CheckStatus.WARNING
+            git_remotes = git_get_remotes()
+            if 'upstream' not in git_remotes.keys() or QMK_FIRMWARE_UPSTREAM not in git_remotes['upstream'].get('url', ''):
+                cli.log.warning('{fg_yellow}The official repository does not seem to be configured as git remote "upstream".')
+                status = CheckStatus.WARNING
+            else:
+                git_deviation = git_check_deviation(git_branch)
+                if git_branch in ['master', 'develop'] and git_deviation:
+                    cli.log.warning('{fg_yellow}The local "%s" branch contains commits not found in the upstream branch.', git_branch)
+                    status = CheckStatus.WARNING
+
+    return status
+
+
 @cli.argument('-y', '--yes', action='store_true', arg_only=True, help='Answer yes to all questions.')
 @cli.argument('-n', '--no', action='store_true', arg_only=True, help='Answer no to all questions.')
 @cli.subcommand('Basic QMK environment checks')
@@ -49,12 +81,11 @@ def doctor(cli):
 
     status = os_tests()
 
-    # Make sure our QMK home is a Git repo
-    git_ok = check_git_repo()
+    status = git_tests()
 
-    if git_ok == CheckStatus.WARNING:
-        cli.log.warning("QMK home does not appear to be a Git repository! (no .git folder)")
-        status = CheckStatus.WARNING
+    venv = in_virtualenv()
+    if venv:
+        cli.log.info('CLI installed in virtualenv.')
 
     # Make sure the basic CLI tools we need are available and can be executed.
     bin_ok = check_binaries()
diff --git a/lib/python/qmk/commands.py b/lib/python/qmk/commands.py
index 104c87545..8ff8501bf 100644
--- a/lib/python/qmk/commands.py
+++ b/lib/python/qmk/commands.py
@@ -2,6 +2,7 @@
 """
 import json
 import os
+import sys
 import shutil
 from pathlib import Path
 from subprocess import DEVNULL
@@ -10,7 +11,7 @@ from time import strftime
 from milc import cli
 
 import qmk.keymap
-from qmk.constants import KEYBOARD_OUTPUT_PREFIX
+from qmk.constants import QMK_FIRMWARE, KEYBOARD_OUTPUT_PREFIX
 from qmk.json_schema import json_load
 
 time_fmt = '%Y-%m-%d-%H:%M:%S'
@@ -237,3 +238,71 @@ def parse_configurator_json(configurator_file):
             user_keymap['layout'] = aliases[orig_keyboard]['layouts'][user_keymap['layout']]
 
     return user_keymap
+
+
+def git_check_repo():
+    """Checks that the .git directory exists inside QMK_HOME.
+
+    This is a decent enough indicator that the qmk_firmware directory is a
+    proper Git repository, rather than a .zip download from GitHub.
+    """
+    dot_git_dir = QMK_FIRMWARE / '.git'
+
+    return dot_git_dir.is_dir()
+
+
+def git_get_branch():
+    """Returns the current branch for a repo, or None.
+    """
+    git_branch = cli.run(['git', 'branch', '--show-current'])
+    if not git_branch.returncode != 0 or not git_branch.stdout:
+        # Workaround for Git pre-2.22
+        git_branch = cli.run(['git', 'rev-parse', '--abbrev-ref', 'HEAD'])
+
+    if git_branch.returncode == 0:
+        return git_branch.stdout.strip()
+
+
+def git_is_dirty():
+    """Returns 1 if repo is dirty, or 0 if clean
+    """
+    git_diff_staged_cmd = ['git', 'diff', '--quiet']
+    git_diff_unstaged_cmd = [*git_diff_staged_cmd, '--cached']
+
+    unstaged = cli.run(git_diff_staged_cmd)
+    staged = cli.run(git_diff_unstaged_cmd)
+
+    return unstaged.returncode != 0 or staged.returncode != 0
+
+
+def git_get_remotes():
+    """Returns the current remotes for a repo.
+    """
+    remotes = {}
+
+    git_remote_show_cmd = ['git', 'remote', 'show']
+    git_remote_get_cmd = ['git', 'remote', 'get-url']
+
+    git_remote_show = cli.run(git_remote_show_cmd)
+    if git_remote_show.returncode == 0:
+        for name in git_remote_show.stdout.splitlines():
+            git_remote_name = cli.run([*git_remote_get_cmd, name])
+            remotes[name.strip()] = {"url": git_remote_name.stdout.strip()}
+
+    return remotes
+
+
+def git_check_deviation(active_branch):
+    """Return True if branch has custom commits
+    """
+    cli.run(['git', 'fetch', 'upstream', active_branch])
+    deviations = cli.run(['git', '--no-pager', 'log', f'upstream/{active_branch}...{active_branch}'])
+    return bool(deviations.returncode)
+
+
+def in_virtualenv():
+    """Check if running inside a virtualenv.
+    Based on https://stackoverflow.com/a/1883251
+    """
+    active_prefix = getattr(sys, "base_prefix", None) or getattr(sys, "real_prefix", None) or sys.prefix
+    return active_prefix != sys.prefix
diff --git a/lib/python/qmk/constants.py b/lib/python/qmk/constants.py
index be5ce5d4e..1078f4ad5 100644
--- a/lib/python/qmk/constants.py
+++ b/lib/python/qmk/constants.py
@@ -6,6 +6,9 @@ from pathlib import Path
 # The root of the qmk_firmware tree.
 QMK_FIRMWARE = Path.cwd()
 
+# Upstream repo url
+QMK_FIRMWARE_UPSTREAM = 'qmk/qmk_firmware'
+
 # This is the number of directories under `qmk_firmware/keyboards` that will be traversed. This is currently a limitation of our make system.
 MAX_KEYBOARD_SUBFOLDERS = 5