The present invention provides for a rules-based system for managing the configuration of electronic mail (email) and/or messaging servers within an enterprise. Rules can be created and implemented that are unique to the enterprise's environment. Embodiments of the present invention provide for checking the current, “live” configuration settings of a mail/message server by applying the applicable rules in the rules database to the current settings. As a result of executing the compliance check, settings that are non-compliant are identified. System configuration may allow for non-compliant settings to be automatically re-configured so as to be compliant with the rule, or the user may be provided with options to authorize automated reconfiguration of all non-compliant settings or select which non-compliant settings that the user desires to re-configure.