[20] Jason Schreier, one of Kotaku's writers since 2012 known for his investigative in-depth coverage of working conditions at various studios and development histories for various video games, announced his departure from the site on April 16, 2020, citing the issues surrounding G/O Media which filtered into disruptions at their sister website Deadspin around October 2019.

[29][30] Jen Glennon resigned her position as editor in March 2024, citing an opposition to G/O Media's desire for the site to deprioritize news and instead focus on producing game guides.

[31] In July 2024, it was reported that Kotaku Australia would shut down as part of a cost-cutting effort from third-party publisher Pedestrian Group.

[33] In 2007, attorney Jack Thompson sued Gawker Media and site editor Brian Crecente over concerns that Kotaku declined to remove threatening user comments,[34] but the lawsuit was dismissed the next day.

[35] In 2010, Kotaku criticized Japanese magazine Famitsu's glowing endorsement of Konami's PlayStation Portable game Metal Gear Solid: Peace Walker as a conflict of interest.

[36] On October 9, 2021, Kotaku published an article about Metroid Dread, which had been released a day prior, running on Nintendo Switch emulators.

[43] In 2007, Kotaku ran a story about rumored upcoming features on the PlayStation 3, and Sony responded by temporarily blacklisting the website.

Further controversy followed when then senior writer Luke Plunkett posted a picture of a fighter plane with victory markings featuring the Imperial Japanese flag.

[51][52] Its creator attempted to shut it down in 2018, claiming that it had become "infested with racism and sexism", but it was reinstated by a Reddit administrator due to the site's guidelines.

[53][54] In March 2024, the narrative development studio Sweet Baby Inc. became the target of claims from online users who said that it promoted a "woke agenda".