diff --git a/CHANGES.rst b/CHANGES.rst
index 118751e9..4ed3c42c 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -17,6 +17,8 @@ Unreleased
     about resource limits to the security page. :issue:`5625`
 -   Add support for the ``Partitioned`` cookie attribute (CHIPS), with the
     ``SESSION_COOKIE_PARTITIONED`` config. :issue`5472`
+-   Give priority to file specified through the -e/--env-file option
+    over default .env & .flaskenv files in CLI.
 
 
 Version 3.0.3
diff --git a/src/flask/cli.py b/src/flask/cli.py
index 8e72db5a..1c8cfb21 100644
--- a/src/flask/cli.py
+++ b/src/flask/cli.py
@@ -528,6 +528,10 @@ class FlaskGroup(AppGroup):
         directory to the directory containing the first file found.
     :param set_debug_flag: Set the app's debug flag.
 
+    .. versionchanged:: 3.1.0
+        Environment file specified through -e/--env-file gets
+        prioity over default .env, .flaskenv files
+
     .. versionchanged:: 2.2
         Added the ``-A/--app``, ``--debug/--no-debug``, ``-e/--env-file`` options.
 
@@ -654,17 +658,23 @@ class FlaskGroup(AppGroup):
         # when importing, blocking whatever command is being called.
         os.environ["FLASK_RUN_FROM_CLI"] = "true"
 
-        # Attempt to load .env and .flask env files. The --env-file
-        # option can cause another file to be loaded.
-        if get_load_dotenv(self.load_dotenv):
-            load_dotenv()
-
         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
             )
 
-        return super().make_context(info_name, args, parent=parent, **extra)
+        # The make_context function goes ahead to parse the arguments
+        # which also includes the -e option. Since that option gets
+        # priority over default config files (See #5532), we need to
+        # call this before attempting to load the default config.
+        ctx = super().make_context(info_name, args, parent=parent, **extra)
+
+        # Attempt to load .env and .flask env files. The --env-file
+        # option can cause another file to be loaded.
+        if get_load_dotenv(self.load_dotenv):
+            load_dotenv()
+
+        return ctx
 
     def parse_args(self, ctx: click.Context, args: list[str]) -> list[str]:
         if not args and self.no_args_is_help:
diff --git a/tests/test_apps/.customenv b/tests/test_apps/.customenv
new file mode 100644
index 00000000..58d7a729
--- /dev/null
+++ b/tests/test_apps/.customenv
@@ -0,0 +1,4 @@
+FOO=customenv
+BAZ=1
+BAR=custombar
+EGGS=custom
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 09995488..2b662233 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -565,6 +565,21 @@ def test_disable_dotenv_from_env(monkeypatch, runner):
     assert "FOO" not in os.environ
 
 
+@need_dotenv
+def test_custom_dotenv_takes_priority(monkeypatch, runner):
+    monkeypatch.chdir(test_path)
+    runner.invoke(FlaskGroup(), "-e .customenv")
+
+    # .customenv is loaded
+    assert "BAZ" in os.environ
+
+    # .customenv takes priority over .flaskenv
+    assert os.environ["BAR"] == "custombar"
+
+    # .customenv takes priority over .env
+    assert os.environ["FOO"] == "customenv"
+
+
 def test_run_cert_path():
     # no key
     with pytest.raises(click.BadParameter):