I’ve solved this myself by adding the following to my theme’s functions.php:
function acf_apply_content_filter_for_api($value, $post_id, $field){
return str_replace( ']]>', ']]>', apply_filters( 'the_content', $value) );
}
function add_content_filter_ACF(){
if(!is_admin()){
remove_all_filters('acf/format_value/type=wysiwyg');
add_filter('acf/format_value/type=wysiwyg', 'acf_apply_content_filter_for_api', 10, 3);
}
}
add_action('init', 'add_content_filter_ACF');