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. Samanosuke and Jacques can gain elemental weapons, changing their fighting style and allowing access to magical attacks. 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. Players also get to control Michelle, who relies on firearms.
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.
New to this game is a focus on time travel when solving puzzles. For example, if Samanosuke comes across a door in the present that has become too withered to open, Jacques will need to open the door in the past so that it will stay open for Samanosuke to progress. Things Samanosuke does in the present will not affect things in the past. However, Ako is able to transfer some items between both timelines.