Ubisoft made a conscious effort to avoid tropes associated with romanticized views of pirates such as crossbones, hooks, and walking the plank, in favor of creating a “grounded sense of realism, of brutality.” They looked to the films "Master and Commander: The Far Side of the World" and "The Mission", as well as the television series "Deadwood" for inspiration, and wanted the city of Havana to display more of the citizens' daily lives than the presence of the pirates because according to the game's lead writer Darby McDevitt: "There are pirates in this world, but it’s a much bigger world than just pirates." As a result of these imposed standards, the possibility of the Hookblade from Assassin's Creed: Revelations returning was shut down by McDevitt immediately after it was suggested by one of the developers for inclusion in the game.

A slightly different cutscene will initiate if Spoiler:Edward leaves Mary Read's body behind in the area between the prison and the boat.

A covered well can be found in the naval fort of Punta Guarico. It's possible to hear pleading pirates from within the well that have been imprisoned there.

There was originally going to be a mission that took place during Mary Read and Anne Bonny's last battle before they were captured, which would have also lead to Edward being captured. However, the developers thought that the player had already spent enough time in Nassau (where the battle was to take place) and the mission was dropped.

Originally, the story was going to center around Edward growing up around pirates in the span of about 20 or 30 years, starting when he was 12 in the William Kidd and Henry Avery era (around 1699) and go on into the Blackbeard era (around 1716). Since both Ezio and Connor went though a similar idea (with mixed results from the fans and developers), they decided to only focus on about a decade starting in 1715, so that Edward is a young man all the way though the game, but still have him go through a tremendous arc.

Two books were big references in the development of the game. The first book was "The General History of Pyrates," which provided a solid historical foundation for the game to use, as well using a German style of capitalizing all nouns, which Ubisoft used in the game's subtitles. The second book was "The Republic of Pirates," which helped the team establish the hub town, real life Nassau, which was a famous stopping point for pirates. The book's author, Colin Woodard, was so much of a influence that he was asked to join the development team to make the game more accurate.