When it was announced that Jonathan Dumont was working on the game, many Ubisoft Quebec employees reportedly refused to work with him (with some even outright quitting) due to past allegations involving abuse and sexual misconduct. In response, Ubisoft CEO Yves Guillemot stated that they take all allegations "extremely seriously", and that Dumont had been "appropriately disciplined" and cleared to continue working.

One of the game's dual protagonists Yasuke, an African samurai, is the first main character in the series to be based on a real historical figure, but his real-life identity and status serving under Japanese daimyo Oda Nobunaga has been the subject of a contentious debate among historians. There are few scholarly/historical resources available describing him and his life, and no known resources from when he was alive that refer to him as a samurai, with the most common belief being his title was a retainer.

His reveal as a lead in the game on May 15, 2024 caused polarizing reactions worldwide on social media. Fans critical of the decision claimed Ubisoft were going against the series' penchant for accurate historical backgrounds and misrepresented Japan, which the series had never covered in-depth, by inflating Yasuke's role in history and not having both protagonists be Japanese (the other protagonist, Naoe, is Japanese), claiming he was not actually a samurai. Fans in support of his role claiming he was actually a samurai called these objections racist and based on narrow-minded arguments and inferences, with some claiming that Asian samurai protagonists in media were oversaturated and that complaints would be the same if the game was set in Africa and starred an African protagonist. This intense fighting led to an edit war on Yasuke's English Wikipedia article, with administrators publicly calling its Talk page "a complete dumpster fire". As of July 3, the consensus that the Talk page reached appears to be that the available historical resources are inconclusive as to if he was or was not a samurai, but that scholars consistently describe Yasuke as a samurai without any sources found where scholars do not describe him as one.

This lack of clarity allows popular media to take creative liberties in adapting him, often depicting him as a high-ranking samurai, and Ubisoft seemed to take a similar direction from the outset. A press release at the game's announcement stated:


Despite the header used, the quote is carefully worded to stop short of directly calling Yasuke a samurai, with more advertising describing him as a "samurai of historical legend". Game director Charles Benoit later acknowledged his life "is surrounded by mysteries" and that "[Yasuke] told us to tell" his story seen in the game, which was also described by associate narrative director Brooke Davies as historical fiction.

Creative director Jonathan Dumont stated in interviews with Famitsu on May 15 that they chose Yasuke to fit with the story of a foreigner who fights off oppressing forces like the Portuguese slave trade, while exploring a country unknown to him alongside the player, stating that they were "first looking for "our samurai," someone who could be our non-Japanese eyes". The following day, the interviews were edited to remove this quote, and to change quotes either directly or contextually referring to Yasuke as an "outsider" to being a "foreign-born samurai". After further mounting controversy, Ubisoft posted a statement to Twitter in English and Japanese on July 23 apologizing for elements in their promotional materials that "caused concern within the Japanese community", reiterating that the game's story was intended to be historical fiction and not an accurate recreation of events, and that Yasuke's real-life status was "a matter of debate and discussion". The Japanese statement received Community Notes pointing out that the stance taken was contradictory, citing several quotes from both the Famitsu interviews and an Xbox interview that emphasized confirming historical accuracy, but was removed from the statement hours later.