In September 2020, it was announced that the game's original director and series creator Michel Ancel would be retiring from the video game industry to focus on working for a wildlife sanctuary, but it was assured that development would continue without him. Later that month, the French newspaper "Libération" reported that several members of his team at Ubisoft Montpellier had accused him of acting abusive and unorganized, resulting in numerous delays and restarts since the game's announcement in 2008. This behavior was allegedly worsened by his simultaneous work on Wild (a big-budget game announced in 2014), preventing him from working on Beyond Good & Evil 2 with its team full-time. Although reports were submitted to company leadership as early as 2017, it was alleged that Ancel's relationship with Ubisoft co-founder Yves Guillemot prevented any major corrections from occurring until June and July 2020, when employees from all over the company came forward with sexual abuse and other misconduct allegations against high-ranking executives. Ubisoft would later comment that Ancel had not been directly involved in the game's development for "some time now" before his departure.

Ancel was interviewed as part of Libération's investigation. He claimed that Guillemot informed him that Ubisoft was investigating him in early August 2020, but claimed he was unaware that numerous team members blamed him for the game's development issues, and believed they were actually caused by long-term stress and burnout. He claimed to have resigned on his own accord and that his only regret was not finishing the game sooner. The newspaper claimed that the interview took place on September 18th, the same day that Ancel and Ubisoft's statements about the departure were released. One week later when the report and interview were published, Ancel denied all of the allegations in an Instagram post, calling the articles "fake news" and accusing the newspaper of publishing them as soon as possible to conflate them with the earlier Ubisoft allegations in June and July, over a month before Ubisoft's investigation into him allegedly began.