Prey is a first-person shooter with role-playing and stealth elements set in an open world environment. The player takes the role of Morgan Yu, a human aboard a space station with numerous species of hostile aliens known collectively as the Typhon. The player is able to select certain attributes of Morgan, including gender, and decisions made by the player that affects elements of the game's story. To survive, the player must collect and use weapons and resources aboard the station to fend off and defeat the Typhon. According to creative director Raphaël Colantonio, the station is completely continuous rather than having separate levels or missions, at times requiring the player to return to areas they previously explored. The player is able to venture outside of the station in space and find shortcuts connecting parts of the station. Colantonio stated that the aliens have an array of different powers that the player character can gain over time; one such alien has the ability to shape shift into everyday items, such as a chair. The player can acquire aliens' abilities by using a device called a psychoscope. Recyclers can be used to break down almost any object into raw materials.
The game has multiple endings, according to lead designer Ricardo Bare; the endings fall into three major narrative structures depending on how the player broadly interacted with the station and surviving humans, but Bare said there are "tons of little permutations" based on specific events.