The game features three main cities; Havana, Kingston, and Nassau, which reside under Spanish, British, and pirate influence, respectively. The game also features 50 other individual locations—including atolls, sea forts, Mayan ruins, sugar plantations and underwater shipwrecks—to explore, with a 60/40 balance between land and naval exploration. Assassin's Creed IV has a more open world feel, with missions similar to those found in Assassin's Creed, as well as fewer restrictions for the player. The world opens up sooner in the game, as opposed to Assassin's Creed III, which had very scripted missions and did not give players freedom to explore until the game was well into its first act. The player will encounter jungles, forts, ruins, and small villages and the world is built to allow players much more freedom, such as allowing players to engage, board, and capture passing ships and swimming to nearby beaches in a seamless fashion. In addition, the hunting system has been retained from Assassin's Creed III, allowing the player to hunt on land, and fish in the water, with resources gathered used to upgrade equipment.

A new aspect in the game is the Jackdaw, the ship that the player captains. The Jackdaw is upgradeable throughout the game, and is easily accessible to the player when needed. In addition, a new underwater component has been added. The player has access to a spyglass, allowing the examination of distant ships, along with their cargo and strength. It can also help determine if an island still has animals to hunt, treasures to find, high points to reach for synchronization or additional side-quests to complete, such as assassinations and naval contracts. An updated form of the recruit system introduced in Assassin's Creed: Brotherhood has returned, allowing Edward to recruit crew members. While Kenway's crew will remain loyal to him, can be promoted to captain acquired ships, and are needed to assist in boarding enemy vessels, they cannot assist in combat or perform long-range assassinations, as in previous games. Ubisoft removed this aspect of the brotherhood system, believing it allowed players to bypass tense and challenging scenarios too easily.

In the present day, at the offices of Abstergo Entertainment—a subsidiary of Abstergo Industries—in Montreal, Quebec, players engage in modern day pirating through the exploration of Abstergo's offices, eavesdropping and hacking, all without combat. As well, various "hacking" games, similar to previous cluster and glyph puzzles, are present, that uncover secrets about Abstergo.

Multiplayer also returns, with new settings and game modes, though it is only land-based.