In the months after Starfleet and the Bajoran Government took command of Deep Space Nine, quickly upgraded the station.

The Cardassian systems that underwent the greatest modifications include the following:

    * EPS power system- All interfaces to Starfleet devices were configured with step-up plasma phase inverters. EPS level limiters, and variable auto-input controllers. Not all of these power-controlling measures were effective at first, but subsequent repairs and upgrades have brought station operations up to an acceptable level of reliability.

    * Atmospheric handling systems- By and large, the Cardassians maintained a living environment that was too hot and dry a compared to that deemed comfortable by other humanoid species. Starfleet and Bajoran engineers reconfigured the environmental control systems for the station's common areas to produce twenty-two degrees Celsius and 18% humidity conditions, and left the remaining controls in private residences and secure work areas to be regulated by individual users.

    * Computer systems- As in the case of the power conversions, the onboard isolinear-based computer systems required a complex set of adaptive interface devices to work with Starfleet systems and programming.

    * Weapons systems- Large-scale Starfleet shield energy generators were installed as backups for the existing defensive shield system. These generators could produce a variety of field and particle types and were interfaced with the Cardassian systems via redundant step-up EPS couplings. New phaser emitters were installed into the existing weapon sail towers, as were magazines and launchers for standard photon torpedoes. Rotary phaser and torpedo launchers were subsequently installed in spaces once used as monitoring and observation facilities.

    * Spacecraft docks and repairs bays- Since not all starships operating in the galaxy conform to all docking ports, modifications had to be made to many of the berthing facilities on Deep Space 9 to accept Starfleet hatch fittings. The most extensive work was done on the six pylon docking ports, three large Docking Ring ports, and the new runabout launch bays.