Jagged Alliance Online will be built around the familiar Jagged Alliance games mechanics, which are a mixture of turn-based battles and real-time action. The player takes control of a group of soldiers, commanding them from an isometric perspective to complete tasks in order to earn cash as well as renown. If a player wants to stay on top, mercenaries will need to be trained and equipped with better weapons. If that's not quite enough, then mercenaries can be borrowed from friends or alliances can be formed with other players.

The advent of open beta testing will also bring a number of new features to the game: Defeated opponents now drop loot that can be collected by the mercenaries during the mission. When a player aims at an explosive barrel or crate, the explosion radius will be shown, making it easier to judge to results of one’s actions. Aiming at an opponent will now show which direction he is most vulnerable from.