diff --git a/aiida/cmdline/commands/cmd_config.py b/aiida/cmdline/commands/cmd_config.py
index f0a045d145..6ac6ef9dd7 100644
--- a/aiida/cmdline/commands/cmd_config.py
+++ b/aiida/cmdline/commands/cmd_config.py
@@ -143,7 +143,7 @@ def verdi_config_set(ctx, option, value, globally, append, remove):
         if not isinstance(current, list):
             echo.echo_critical(f'cannot append/remove to value: {current}')
         if append:
-            value = current + [value]
+            value = list(set(current + [value]))
         else:
             value = [item for item in current if item != value]
 
diff --git a/tests/cmdline/commands/test_config.py b/tests/cmdline/commands/test_config.py
index 39d81185b8..eac3d10e2b 100644
--- a/tests/cmdline/commands/test_config.py
+++ b/tests/cmdline/commands/test_config.py
@@ -49,10 +49,10 @@ def test_config_append_option(run_cli_command, config_with_profile_factory):
     """Test the `verdi config set --append` command when appending an option value."""
     config = config_with_profile_factory()
     option_name = 'caching.enabled_for'
-    for value in ['x', 'y']:
+    for value in ['x', 'y', 'x', 'y']:
         options = ['config', 'set', '--append', option_name, value]
         run_cli_command(cmd_verdi.verdi, options, use_subprocess=False)
-    assert config.get_option(option_name, scope=get_profile().name) == ['x', 'y']
+    assert sorted(config.get_option(option_name, scope=get_profile().name)) == ['x', 'y']
 
 
 def test_config_remove_option(run_cli_command, config_with_profile_factory):
@@ -60,7 +60,7 @@ def test_config_remove_option(run_cli_command, config_with_profile_factory):
     config = config_with_profile_factory()
 
     option_name = 'caching.disabled_for'
-    config.set_option(option_name, ['x', 'y'], scope=get_profile().name)
+    config.set_option(option_name, ['x', 'x', 'y', 'x'], scope=get_profile().name)
 
     options = ['config', 'set', '--remove', option_name, 'x']
     run_cli_command(cmd_verdi.verdi, options, use_subprocess=False)