How to add another condition to a specific active facet?
The solution is quite simple :

function mymodule_search_api_query_alter(SearchApiQueryInterface $query) {
    if(preg_match('/PRETTYPATHID/',url($_GET['q']))){
        $base_filter = $query-&gt;createFilter('AND');
        $base_filter-&gt;condition('MYFIELD', NULL, "&lt;&gt;");
        $query-&gt;filter($base_filter);
    }

}