During each round, players take turns selecting a role card from those on the table (such as "Trader" or "Builder"). When a role is chosen, every player gets to take the action associated with that role. The player who selected the role also receives a small privilege for doing so; for example, choosing the "Builder" role allows all players to construct a building, but the player who chose the role may do so at a discount on that turn. Unused roles gain a doubloon bonus at the end of each turn, and the next player who chooses that role gets to keep any doubloon bonus associated with it. This encourages players to make use of all the roles throughout a typical course of a game.

Puerto Rico 1897 uses a variable phase order mechanism in which a token is passed clockwise to the next player at the conclusion of a turn. The player with the token begins the round by choosing a role and taking the first action.

Players earn victory points for owning buildings, for shipping goods, and for occupied "large buildings". Each player's accumulated shipping chips are kept face down and come in denominations of one or five. This prevents other players from being able to determine the exact score of another player. Goods and doubloons are placed in clear view of other players, and the totals of each can always be requested by a player. As the game enters its later stages, the unknown quantity of shipping tokens and its denominations require players to consider their options before choosing a role that can end the game.