If you switch your virtual host from FCGId to PHP-FPM in Virtualmin you cannot use your php values settings from /home/[virtualhost_name]/etc/php.ini like in FCGId.
Loading a php file with phpinfo() function content Loaded Configuration will be equal to /etc/php/[version]/fpm/php.ini. In this case all your virtual hosts using PHP-FPM will use one single configuration file.
In case you need to override some php values Virtualmin is creating a file in /etc/php[version]/fpm/pool.d/[virtualhost_number].conf. Values format should be like this "php_admin_value[allow_url_fopen] = 0". Once you load the phpinfo file in browser this values will override the default ones.
Unfortunately you have to do this manually in Terminal. Virtualmin doesn't have this feature to edit in a section of your virtual host the pool file content. I suggested this in Issues section but someone closed and marked it as fixed. I agree it is a feature request but an important one.
I can do this by my own but other cannot do it.