diff --git a/CHANGES.rst b/CHANGES.rst
index ce85e67340..84ffbf0618 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -25,6 +25,9 @@ Unreleased
 -   Added the ``View.init_every_request`` class attribute. If a view
     subclass sets this to ``False``, the view will not create a new
     instance on every request. :issue:`2520`.
+-   A ``flask.cli.FlaskGroup`` Click group can be nested as a
+    sub-command in a custom CLI. :issue:`3263`
+
 
 Version 2.1.3
 -------------
diff --git a/src/flask/app.py b/src/flask/app.py
index 65e95623d6..360916dbf5 100644
--- a/src/flask/app.py
+++ b/src/flask/app.py
@@ -10,6 +10,7 @@
 from threading import Lock
 from types import TracebackType
 
+import click
 from werkzeug.datastructures import Headers
 from werkzeug.datastructures import ImmutableDict
 from werkzeug.exceptions import Aborter
@@ -23,6 +24,7 @@
 from werkzeug.routing import RequestRedirect
 from werkzeug.routing import RoutingException
 from werkzeug.routing import Rule
+from werkzeug.serving import is_running_from_reloader
 from werkzeug.urls import url_quote
 from werkzeug.utils import redirect as _wz_redirect
 from werkzeug.wrappers import Response as BaseResponse
@@ -908,12 +910,18 @@ def run(
             The default port is now picked from the ``SERVER_NAME``
             variable.
         """
-        # Change this into a no-op if the server is invoked from the
-        # command line. Have a look at cli.py for more information.
+        # Ignore this call so that it doesn't start another server if
+        # the 'flask run' command is used.
         if os.environ.get("FLASK_RUN_FROM_CLI") == "true":
-            from .debughelpers import explain_ignored_app_run
+            if not is_running_from_reloader():
+                click.secho(
+                    " * Ignoring a call to 'app.run()', the server is"
+                    " already being run with the 'flask run' command.\n"
+                    "   Only call 'app.run()' in an 'if __name__ =="
+                    ' "__main__"\' guard.',
+                    fg="red",
+                )
 
-            explain_ignored_app_run()
             return
 
         if get_load_dotenv(load_dotenv):
diff --git a/src/flask/cli.py b/src/flask/cli.py
index 77c1e25a9c..a4e366d7c7 100644
--- a/src/flask/cli.py
+++ b/src/flask/cli.py
@@ -5,12 +5,14 @@
 import re
 import sys
 import traceback
+import typing as t
 from functools import update_wrapper
 from operator import attrgetter
 from threading import Lock
 from threading import Thread
 
 import click
+from werkzeug.serving import is_running_from_reloader
 from werkzeug.utils import import_string
 
 from .globals import current_app
@@ -273,7 +275,7 @@ def __init__(self, loader, use_eager_loading=None):
         self._bg_loading_exc = None
 
         if use_eager_loading is None:
-            use_eager_loading = os.environ.get("WERKZEUG_RUN_MAIN") != "true"
+            use_eager_loading = not is_running_from_reloader()
 
         if use_eager_loading:
             self._load_unlocked()
@@ -477,7 +479,13 @@ def __init__(
         if add_version_option:
             params.append(version_option)
 
-        AppGroup.__init__(self, params=params, **extra)
+        if "context_settings" not in extra:
+            extra["context_settings"] = {}
+
+        extra["context_settings"].setdefault("auto_envvar_prefix", "FLASK")
+
+        super().__init__(params=params, **extra)
+
         self.create_app = create_app
         self.load_dotenv = load_dotenv
         self.set_debug_flag = set_debug_flag
@@ -545,26 +553,22 @@ def list_commands(self, ctx):
 
         return sorted(rv)
 
-    def main(self, *args, **kwargs):
-        # Set a global flag that indicates that we were invoked from the
-        # command line interface. This is detected by Flask.run to make the
-        # call into a no-op. This is necessary to avoid ugly errors when the
-        # script that is loaded here also attempts to start a server.
-        os.environ["FLASK_RUN_FROM_CLI"] = "true"
-
+    def make_context(
+        self,
+        info_name: t.Optional[str],
+        args: t.List[str],
+        parent: t.Optional[click.Context] = None,
+        **extra: t.Any,
+    ) -> click.Context:
         if get_load_dotenv(self.load_dotenv):
             load_dotenv()
 
-        obj = kwargs.get("obj")
-
-        if obj is None:
-            obj = ScriptInfo(
+        if "obj" not in extra and "obj" not in self.context_settings:
+            extra["obj"] = ScriptInfo(
                 create_app=self.create_app, set_debug_flag=self.set_debug_flag
             )
 
-        kwargs["obj"] = obj
-        kwargs.setdefault("auto_envvar_prefix", "FLASK")
-        return super().main(*args, **kwargs)
+        return super().make_context(info_name, args, parent=parent, **extra)
 
 
 def _path_is_ancestor(path, other):
@@ -637,7 +641,7 @@ def show_server_banner(env, debug, app_import_path, eager_loading):
     """Show extra startup messages the first time the server is run,
     ignoring the reloader.
     """
-    if os.environ.get("WERKZEUG_RUN_MAIN") == "true":
+    if is_running_from_reloader():
         return
 
     if app_import_path is not None:
@@ -653,10 +657,10 @@ def show_server_banner(env, debug, app_import_path, eager_loading):
     if env == "production":
         click.secho(
             "   WARNING: This is a development server. Do not use it in"
-            " a production deployment.",
+            " a production deployment.\n   Use a production WSGI server"
+            " instead.",
             fg="red",
         )
-        click.secho("   Use a production WSGI server instead.", dim=True)
 
     if debug is not None:
         click.echo(f" * Debug mode: {'on' if debug else 'off'}")
@@ -963,6 +967,7 @@ def routes_command(sort: str, all_methods: bool) -> None:
 
 
 cli = FlaskGroup(
+    name="flask",
     help="""\
 A general utility script for Flask applications.
 
@@ -978,7 +983,7 @@ def routes_command(sort: str, all_methods: bool) -> None:
 """.format(
         cmd="export" if os.name == "posix" else "set",
         prefix="$ " if os.name == "posix" else "> ",
-    )
+    ),
 )
 
 
diff --git a/src/flask/debughelpers.py b/src/flask/debughelpers.py
index 27d378c24a..b1e3ce1bc7 100644
--- a/src/flask/debughelpers.py
+++ b/src/flask/debughelpers.py
@@ -1,6 +1,4 @@
-import os
 import typing as t
-from warnings import warn
 
 from .app import Flask
 from .blueprints import Blueprint
@@ -159,16 +157,3 @@ def explain_template_loading_attempts(app: Flask, template, attempts) -> None:
         info.append("  See https://flask.palletsprojects.com/blueprints/#templates")
 
     app.logger.info("\n".join(info))
-
-
-def explain_ignored_app_run() -> None:
-    if os.environ.get("WERKZEUG_RUN_MAIN") != "true":
-        warn(
-            Warning(
-                "Silently ignoring app.run() because the application is"
-                " run from the flask command line executable. Consider"
-                ' putting app.run() behind an if __name__ == "__main__"'
-                " guard to silence this warning."
-            ),
-            stacklevel=3,
-        )
diff --git a/tests/test_cli.py b/tests/test_cli.py
index c9dd5ade06..7a8e9af9cb 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -388,6 +388,19 @@ def test():
     assert result.output == f"{not set_debug_flag}\n"
 
 
+def test_flaskgroup_nested(app, runner):
+    cli = click.Group("cli")
+    flask_group = FlaskGroup(name="flask", create_app=lambda: app)
+    cli.add_command(flask_group)
+
+    @flask_group.command()
+    def show():
+        click.echo(current_app.name)
+
+    result = runner.invoke(cli, ["flask", "show"])
+    assert result.output == "flask_test\n"
+
+
 def test_no_command_echo_loading_error():
     from flask.cli import cli