Limitations of ZetaBoards include the lack of FTP access, editing restrictions and inability to access the MySQL database directly, as the software is remotely hosted. Also, e-mail notification of new topics, replies to existing topics and notification of new registrants is not part of the standard ZetaBoard package.
Google AdSense is present on all forums to allow for the free cost to forum admins to host their forums on their own domain.
Users now have the option to purchase ad removal for their forum. After board conversions from InvisionFree to ZetaBoards began, multiple bugs and glitches were found among the converted forums. While the Zathyus team informed its users that converting from ZetaBoards back to InvisionFree would not be possible, many forum owners expressed concern on the company website as to the fact that they are unable to return to InvisionFree due to disappointment with the new system or problems arising from faulty code or lack of support for some skins and themes.