Onimusha 3 is played in a real-time environment instead of pre-rendered backgrounds, although the camera is still controlled by the computer. Gameplay alternates between Samanosuke fighting in modern-day Paris and Jacques fighting in feudal Japan. Samanosuke fights using close range weapons, while Jacques uses an energy whip, which can also be used at certain points to swing across gaps. While Samanosuke cannot swing like Jacques he is able to use a bow in order to perform long-range attacks. Both characters also have defensive skills known as Issen that allows them to instantly kill an enemy by attacking just before the enemy makes contact with its attack.[4]
Samanosuke and Jacques can gain elemental weapons, changing their fighting style and allowing access to magical attacks. Defeating enemies reaps souls, which when absorbed can restore health and magic, be used as currency for purchasing ammunition and health items, and allow Samanosuke or Jacques to enter a more powerful Onimusha state for a short time.[4] If the player collects certain items during the game and completes it, Samanosuke will be able to use his weapons from the first game in the next playthrough. Armors with different properties can be obtained in the game but they require some items in order to work.
During certain portions of the story, players also get to control Michelle, who relies on firearms. Another minigame gives the players control over the lance fighter Heihachiro. Unlike Samanosuke and Jacques, Heihachiro and Michelle do not possess upgradeable weapons and cannot enter the Oni mode.[5]