Project Root is a futuristic top-down shooter where the player controls the F 72 Zonda aircraft. The protagonist is Lance Rockport, a member of the Arcturus rebel group. The neighbourhood where he grew up was demolished because of the expansion plans of the Prometheus Corporation led by Demetrio Watts, which made him join a band of rebels for which he now completes missions. Prometheus has the best technology available and dominates the market. They also provide electricity to the houses of all civilians and Arcturus learns they have sinister plans.
Levels take place in environments that can be explored freely in any direction. The ship always stays in the same position at the bottom of the screen facing the same way, but as it explores and accelerates, turning causes the environment / camera to rotate around the ship, instead of the ship itself. Shown from a top-down view all game elements are in 3D, but the ship can only be guided over a single, horizontal plane.
Three types of weapons can be used. There is a regular cannon with endless ammo, ground fire to target tanks and structures on the ground separately, also with endless ammo, and special weapons that can only be activated after picking up an item often left behind by destroyed enemies. A pair of white cross-hairs shows the general firing direction. A radar mini-map in the bottom left corner of the screen is used to locate objectives. Missions sometimes have secondary objectives and goals can change quickly as they are introduced by characters while playing, with a separate communications panel.
Each level has two difficulty options. The ship has a limited amount of energy and multiple lives. By playing the game experience is gained to level up. Main experience points can be spent on upgrades affecting speed, handling, the standard weapon, special weapons, the airframe and defense.