You can use the koha-run-backups command. This command will generate a koha system backup and a database backup. By default, the backup will be stored in the /var/spool/koha/instancename directory and will be stored for 2 days (that means yesterday backup and today backup).
You can also change the default configuration. For that, see reference https://wiki.koha-community.org/wiki/Commands_provided_by_the_Debian_packages