diff --git a/annif/cli.py b/annif/cli.py
index 979c5bfb1..63a93c795 100644
--- a/annif/cli.py
+++ b/annif/cli.py
@@ -30,6 +30,7 @@
     create_app=create_app, add_default_commands=False, add_version_option=False
 )
 cli = click.version_option(message="%(version)s")(cli)
+cli.params = [opt for opt in cli.params if opt.name not in ("env_file", "app")]
 
 
 @cli.command("list-projects")