Electrosphere plays in a similar manner to its predecessors, but with several additions that would become staples of the series. The camera can be rotated in a 360° range around the player, and a large assortment of weapons, including guns and main missiles, can be chosen freely before each mission. Wingmen cannot be selected, but are instead dictated by the story. Missions combined radio chatter from both allies and enemies to expand the narrative.

Electrosphere is notably the only game in the series that featured a mission set in outer space, complete with a different physics model on the handling of aircraft in a zero-gravity situation.

The Japanese version elaborates on the mission branching mechanics of Ace Combat 2 by allowing the player to join one of four factions through the story. Specific missions gave the player the ability to decide on remaining with one faction or switching to another. The Clear Rank system was expanded upon, where D ranks are specifically earned by failing the mission's main objective but do not require the mission to be restarted. In addition, certain circumstances unlocked hidden missions to be played, similar to AC2.