diff --git a/bench/app.py b/bench/app.py
index 6ca99aab..6886e0a4 100755
--- a/bench/app.py
+++ b/bench/app.py
@@ -308,6 +308,14 @@ Here are your choices:
 				add_to_excluded_apps_txt(app, bench_path=bench_path)
 				print("Skipping pull for app {}, since remote doesn't exist, and adding it to excluded apps".format(app))
 				continue
+
+			if not get_config(bench_path).get('shallow_clone') or not reset:
+				is_shallow = os.path.exists(os.path.join(app_dir, ".git", "shallow"))
+				if is_shallow:
+					s = " to safely pull remote changes." if not reset else ""
+					print(f"Unshallowing {app}{s}")
+					exec_cmd(f"git fetch {remote} --unshallow", cwd=app_dir)
+
 			branch = get_current_branch(app, bench_path=bench_path)
 			logger.log('pulling {0}'.format(app))
 			if reset:
diff --git a/bench/config/common_site_config.py b/bench/config/common_site_config.py
index 41d9cc9c..d7c492bf 100644
--- a/bench/config/common_site_config.py
+++ b/bench/config/common_site_config.py
@@ -8,7 +8,6 @@ import os
 default_config = {
 	'restart_supervisor_on_update': False,
 	'restart_systemd_on_update': False,
-	'auto_update': False,
 	'serve_default_site': True,
 	'rebase_on_pull': False,
 	'frappe_user': getpass.getuser(),
diff --git a/bench/utils.py b/bench/utils.py
index 7bb312ba..93d2bda5 100755
--- a/bench/utils.py
+++ b/bench/utils.py
@@ -112,6 +112,16 @@ def get_env_cmd(cmd, bench_path='.'):
 	return os.path.abspath(os.path.join(bench_path, 'env', 'bin', cmd))
 
 
+def pause_exec(seconds=10):
+	from time import sleep
+
+	for i in range(seconds, 0, -1):
+		print(f"Will continue execution in {i} seconds...", end="\r")
+		sleep(1)
+
+	print(" " * 40, end="\r")
+
+
 def init(path, apps_path=None, no_procfile=False, no_backups=False,
 		frappe_path=None, frappe_branch=None, verbose=False, clone_from=None,
 		skip_redis_config_generation=False, clone_without_update=False, ignore_exist=False, skip_assets=False,
@@ -208,6 +218,16 @@ def update(pull=False, apps=None, patch=False, build=False, requirements=False,
 			print("This update will cause a major version change in Frappe/ERPNext from {0} to {1}. \nThis would take significant time to migrate and might break custom apps.".format(*version_upgrade[1:]))
 			click.confirm('Do you want to continue?', abort=True)
 
+	if not reset and conf.get('shallow_clone'):
+		log("""shallow_clone is set in your bench config.
+However without passing the --reset flag, your repositories will be unshallowed.
+To avoid this, cancel this operation and run `bench update --reset`.
+
+Consider the consequences of `git reset --hard` on your apps before you run that.
+To avoid seeing this warning, set shallow_clone to false in your common_site_config.json
+		""", level=3)
+		pause_exec(seconds=10)
+
 	if version_upgrade[0] or (not version_upgrade[0] and force):
 		validate_upgrade(version_upgrade[1], version_upgrade[2], bench_path=bench_path)
 	conf.update({ "maintenance_mode": 1, "pause_scheduler": 1 })
@@ -221,9 +241,11 @@ def update(pull=False, apps=None, patch=False, build=False, requirements=False,
 		apps = [app.strip() for app in re.split(",| ", apps) if app]
 
 	if pull:
+		print('Updating apps source...')
 		pull_apps(apps=apps, bench_path=bench_path, reset=reset)
 
 	if requirements:
+		print('Setting up requirements...')
 		update_requirements(bench_path=bench_path)
 		update_node_packages(bench_path=bench_path)
 
@@ -232,6 +254,7 @@ def update(pull=False, apps=None, patch=False, build=False, requirements=False,
 		patch_sites(bench_path=bench_path)
 
 	if build:
+		print('Building assets...')
 		build_assets(bench_path=bench_path)
 
 	if version_upgrade[0] or (not version_upgrade[0] and force):