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 Assassin's Creed 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, as well as no known resources from the time he was alive that refer to him as a samurai, with the most common conclusion being his title was a retainer to Nobunaga.

His reveal as a main character 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 had never been covered in-depth in the globally-spanning game series, by inflating Yasuke's role in history and not having both protagonists be Japanese (the other protagonist, Naoe, is Japanese), claiming that Yasuke was not actually a samurai. Fans in support of Yasuke's role claiming that he was actually a samurai called these objections racist and based on narrow-minded arguments and inferences, with some going so far as to claim that Asian samurai protagonists in media were oversaturated and that critics would give the same complaints if it were a game set in Africa starring an African protagonist. This intense fighting led to an edit war on Yasuke's English Wikipedia article, with administrators publicly calling the article's Talk page "a complete dumpster fire". As of May 30, the consensus that was reached on the Talk page appears to be that the available resources are inconclusive, and there is still no historical evidence confirming that Yasuke was or was not a samurai. Reflecting this, the article does not call him a samurai when covering his documented life.

The lack of clarity on his life allowed popular culture and media to take creative liberties in speculating who he was, often depicting him in adaptations as a high-ranking samurai, and Ubisoft seemed to be going in a similar direction. The advertising for the game at its announcement described Yasuke as a "samurai of historical legend", and a press release stated:


While the header for this section of the press release is called "Yasuke: A Real-Life Samurai", this description seems to be carefully worded to stop short of directly calling him a samurai, with the use of "historical legend" elsewhere suggesting that they were aware of the unconfirmed status and were fictionalizing Yasuke for the game.

In a set of developer interviews with Famitsu published on May 15, creative director Jonathan Dumont elaborated that they also chose Yasuke to fit with the game's story of a foreigner who fights off oppressing forces, like the Portuguese slave trade's effects on Japan, 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 Famitsu article was edited to change developer quotes in the interviews that either directly or contextually referred to Yasuke as an "outsider" to being a "foreign-born samurai", and also removed the aforementioned Jonathan Dumont quote, for unknown reasons.