diff --git a/src/aiida/cmdline/commands/cmd_code.py b/src/aiida/cmdline/commands/cmd_code.py
index aa16b91564..477d2f61ab 100644
--- a/src/aiida/cmdline/commands/cmd_code.py
+++ b/src/aiida/cmdline/commands/cmd_code.py
@@ -15,7 +15,6 @@
 
 from aiida.cmdline.commands.cmd_verdi import verdi
 from aiida.cmdline.groups.dynamic import DynamicEntryPointCommandGroup
-from aiida.cmdline.groups.verdi import VerdiCommand
 from aiida.cmdline.params import arguments, options, types
 from aiida.cmdline.params.options.commands import code as options_code
 from aiida.cmdline.utils import echo, echo_tabulate
@@ -90,7 +89,7 @@ def set_code_builder(ctx, param, value):
 # because the ``LABEL`` option has a callback that relies on the computer being already set. Execution order is
 # guaranteed only for the interactive case, however. For the non-interactive case, the callback is called explicitly
 # once more in the command body to cover the case when the label is specified before the computer.
-@verdi_code.command('setup', deprecated='Please use `verdi code create` instead.', cls=VerdiCommand)
+@verdi_code.command('setup', deprecated='Please use `verdi code create` instead.')
 @options_code.ON_COMPUTER()
 @options_code.COMPUTER()
 @options_code.LABEL()
diff --git a/src/aiida/cmdline/commands/cmd_setup.py b/src/aiida/cmdline/commands/cmd_setup.py
index 0063d31d10..0c18ce4238 100644
--- a/src/aiida/cmdline/commands/cmd_setup.py
+++ b/src/aiida/cmdline/commands/cmd_setup.py
@@ -11,14 +11,13 @@
 import click
 
 from aiida.cmdline.commands.cmd_verdi import verdi
-from aiida.cmdline.groups.verdi import VerdiCommand
 from aiida.cmdline.params import options
 from aiida.cmdline.params.options.commands import setup as options_setup
 from aiida.cmdline.utils import decorators, echo
 from aiida.manage.configuration import Profile, load_profile
 
 
-@verdi.command('setup', deprecated='Please use `verdi profile setup` instead.', cls=VerdiCommand)
+@verdi.command('setup', deprecated='Please use `verdi profile setup` instead.')
 @options.NON_INTERACTIVE()
 @options_setup.SETUP_PROFILE()
 @options_setup.SETUP_USER_EMAIL()
diff --git a/src/aiida/cmdline/groups/verdi.py b/src/aiida/cmdline/groups/verdi.py
index 8f0f3abcc5..987baa1c0c 100644
--- a/src/aiida/cmdline/groups/verdi.py
+++ b/src/aiida/cmdline/groups/verdi.py
@@ -81,7 +81,11 @@ def __init__(self, *args, **kwargs):
 
 
 class VerdiCommand(click.Command):
-    """ """
+    """Custom command implementation to change the logic how the deprecation warning is handled. In the parent class the
+    warning is printed only on invocation and after the parsing of the arguments. In this class we print the warning in
+    addition when the help page is printed and change the behavior on invocation. It is printed on invocation before the
+    arguments are parsed. That allows a printing of the deprecation warning with the first prompt requesting missing
+    arguments."""
 
     def parse_args(self, ctx: click.Context, args: t.List[str]) -> t.List[str]:
         if self.deprecated:
@@ -96,7 +100,6 @@ def parse_args(self, ctx: click.Context, args: t.List[str]) -> t.List[str]:
         return super().parse_args(ctx, args)
 
     def invoke(self, ctx: click.Context) -> t.Any:
-        """Overwrites the deprecation warning that is now printed in parse_args"""
         if self.callback is not None:
             return ctx.invoke(self.callback, **ctx.params)
 
@@ -109,6 +112,7 @@ class VerdiCommandGroup(click.Group):
     """
 
     context_class = VerdiContext
+    command_class = VerdiCommand
 
     @staticmethod
     def add_verbosity_option(cmd: click.Command) -> click.Command:
@@ -154,15 +158,6 @@ def get_command(self, ctx: click.Context, cmd_name: str) -> click.Command | None
         cmd = super().get_command(ctx, cmd_name)
 
         if cmd is not None:
-            # if cmd.deprecated:
-            #    import ipdb; ipdb.set_trace()
-            #    # We are abusing click.Command `deprecated` member variable by using a
-            #    # string instead of a bool to also use it as optional deprecated message
-            #    echo_deprecated(
-            #        cmd.deprecated
-            #        if isinstance(cmd.deprecated, str)  # type: ignore[redundant-expr]
-            #        else 'This command is deprecated.'
-            #    )
             return self.add_verbosity_option(cmd)
 
         # If this command is called during tab-completion, we do not want to print an error message if the command can't
diff --git a/tests/cmdline/commands/test_code.py b/tests/cmdline/commands/test_code.py
index a36a7bb28a..8aeeb5cec8 100644
--- a/tests/cmdline/commands/test_code.py
+++ b/tests/cmdline/commands/test_code.py
@@ -46,6 +46,21 @@ def test_help(run_cli_command):
     run_cli_command(cmd_code.setup_code, ['--help'])
 
 
+def test_code_setup_deprecation(run_cli_command):
+    """Checks if a deprecation warning is printed in stdout and stderr."""
+    # Checks if the deprecation warning is present when invoking the help page
+    result = run_cli_command(cmd_code.setup_code, ['--help'])
+    assert 'Deprecated:' in result.output
+    assert 'Deprecated:' in result.stderr
+
+    # Checks if the deprecation warning is present when invoking the command
+    # Runs setup in interactive mode and sends Ctrl+D (\x04) as input so we exit the prompts.
+    # This way we can check if the deprecated message was printed with the first prompt.
+    result = run_cli_command(cmd_code.setup_code, user_input='\x04', use_subprocess=True, raises=True)
+    assert 'Deprecated:' in result.output
+    assert 'Deprecated:' in result.stderr
+
+
 @pytest.mark.usefixtures('aiida_profile_clean')
 def test_code_list_no_codes_error_message(run_cli_command):
     """Test ``verdi code list`` when no codes exist."""
diff --git a/tests/cmdline/commands/test_setup.py b/tests/cmdline/commands/test_setup.py
index 9a12e3fb88..6c7a668542 100644
--- a/tests/cmdline/commands/test_setup.py
+++ b/tests/cmdline/commands/test_setup.py
@@ -40,6 +40,20 @@ def init_profile(self, pg_test_cluster, empty_config, run_cli_command):
         self.pg_test = pg_test_cluster
         self.cli_runner = run_cli_command
 
+    def test_setup_deprecation(self):
+        """Checks if a deprecation warning is printed in stdout and stderr."""
+        # Checks if the deprecation warning is present when invoking the help page
+        result = self.cli_runner(cmd_setup.setup, ['--help'])
+        assert 'Deprecated:' in result.output
+        assert 'Deprecated:' in result.stderr
+
+        # Checks if the deprecation warning is present when invoking the command
+        # Runs setup in interactive mode and sends Ctrl+D (\x04) as input so we exit the prompts.
+        # This way we can check if the deprecation warning was printed with the first prompt.
+        result = self.cli_runner(cmd_setup.setup, user_input='\x04', use_subprocess=True, raises=True)
+        assert 'Deprecated:' in result.output
+        assert 'Deprecated:' in result.stderr
+
     def test_help(self):
         """Check that the `--help` option is eager, is not overruled and will properly display the help message.