SetEnv in .htaccess file doesn't seem to work with PHP-FPM

I'm moving my CodeIgniter project to a new server, which has Apache in event mode with PHP-FPM installed. For some reason, the SetEnv directives in my .htaccess file no longer find their way into PHP:
that CI_ENV value doesn't ever find its way into $_SERVER["CI_ENV"] in php.

Can anyone tell me why this isn't working and what the recommended best practice is for setting this value a php-fpm environment?

This also may apply to CI controllers executed via command line.