The gameplay of Age of Sail II features a minimap, helm, and lists of vessels in play. The player controls one or more vessels each with a specified amount of cannons, health, and sails. There are also controls for speed of the gameplay.

To achieve victory, the player must either cause the enemy ships to surrender, or to simply sink them. Damage inflicted on a vessel is determined by the type of shots fired (round, chain, grape, canister), and the target (hull/sail). Each fire also inflicts damage on the ship's crew. Canister shots are made specifically to inflict damage on crew members. The less the men aboard a ship, the higher chance for the ship to surrender. Speed of activities such as maneuvering the sails, repairing damage, and cannon reload speed are also affected.

The game was accused by reviewers of the time of having an overly complicated and sometimes downright broken interface, with unnecessary complication when directing crews to perform the various actions to keep a vessel in action. The 3-D game engine also came in for criticism, occasionally running as slowly as four frames per second in large fleet actions.