Players control Snake through the game map and attempt to complete missions while avoiding being spotted by the enemy. The threat detection system is revamped, with the removal of the onscreen meter or gauge to indicate the player that they are in the 'alert/evasion/caution' state as in previous games, which have instead been replaced by visual and audio representations. Snake's binoculars have also been revamped; instead of selecting the binoculars as an item, the binoculars are hot keyed to a button. The player is able to mark enemies and be aware of their locations in the iDroid's holographic display. 

Ground Zeroes features seven missions in total, locked at individual levels. After completing the main mission the player will unlock four subsequent missions referred to as Side Ops set at different points in the day, all set in Camp Omega. These missions involve specific tasks, such as eliminating certain targets or obtaining classified information. After achieving a certain objective in the main mission, the player may unlock two additional Extra Op missions.