in my case after installing zabbix from sources (removed zabbix 4.0 because upgrading to 4.2 wasn't possible via apt on a Raspbian GNU/Linux 9.4 stretch) it loaded the config from /usr/local/etc/zabbix_server.conf
instead from /etc/zabbix/zabbix_server.conf
After deleting /usr/local/etc/zabbix_server.conf
and creating a symlink pointing to the correct config file in /etc/zabbix/zabbix_server.conf
it started to work