Autocomplete several fields with values based on the selected value of an user reference field
I just found the solution to my problem: Every AJAX command runs and replaces the defined element. The trick is to predefine the values for all fields I need to update, within the callback. Then, these values remain in tact within the array of the newly rendered fields using the AJAX commands. Here is my updated callback:

function my_ajax_callback(&amp;$form, &amp;$form_state) {
    if (user_load_by_name($form_state['values']['triggering_field_id'][LANGUAGE_NONE][0]['value']) != FALSE) {
        $user_obj = user_load_by_name($form_state['values']['triggering_field_id'][LANGUAGE_NONE][0]['value']);
        $user_id = $user_obj-&gt;uid;
        // and another user attribute:
        $user_whatever_userfield = $user_obj-&gt;whatever;

        $form['dependant_field1'][LANGUAGE_NONE][0]['value']['#value'] = $user_id;
        $form['dependant_field2'][LANGUAGE_NONE][0]['value']['#value'] = $user_whatever_userfield;

        $commands = array();
        $commands[] = ajax_command_replace("#dependant_field1_wrapper", render($form['dependant_field1']));
        $commands[] = ajax_command_replace("#dependant_field2_wrapper", render($form['dependant_field2']));
        return array('#type' =&gt; 'ajax', '#commands' =&gt; $commands);
    }
}


Also, I changed the position of my wrapper to have a wider range, in order to include all the fields I want to ajax-update. As every AJAX command will be recreating each form element, if the form element lives within a wrapper (added in form_alter), the wrapper will also be rendered and that causes an HTML mess. So having one hidden field above &amp; another hidden field below my fields makes life easy. The new wrapper encloses these hidden fields and leaves all other fields clean when regenerated from the callback.