In the anime universe, there are many controversial Isekai anime that have been questioned by fans either on the narrative or on certain visual presentations. While the narrative sometimes drifts into grey territory, the real problem lies when the main characters, especially the protagonists, start showing a problematic side of their personality.
Here are some of the most controversial Isekai anime out there, which have been questioned by fans, especially concerning how the main protagonists act in their series.
Disclaimer: This article reflects the author's opinions and may contain some canon typical mentions of violence/gore/sensitive topics. Readers' discretion is advised.
Arifureta, Overlord, and 8 other controversial Isekai anime with problematic main characters
1) Mushoku Tensei: Jobless Reincarnation- Rudeus Greyrat

The overall Mushoku Tensei: Jobless Reincarnation series has been considered as one of the most popular and well-written storylines in the Isekai anime genre. However, there is a slight problem with Rudeus' character that leads to some controversy early on.
Following the genre's narrative pattern, before Rudeus was isekai'd into a new world, he sowed some perverted tendencies in his previous life, which also carried over into his new life, early on. He was also a socially problematic individual, which raised the eyebrows of many fans towards him as the main character.
However, later in the series, his tendencies gradually disappeared as he grew into his new life; making the fans also forget about his past life, and overall turning the series into a popular hit.
2) Redo of Healer- Keyaru

The Redo of Healer is purely based on a revenge narrative for the main protagonist Keyaru, after he was wronged in his previous life. The anime itself follows a very dark and graphic visual cue with multiple violent scenes and some extensive nudity throughout the season.
Furthermore, Keyaru's path of revenge is also very torturous and violent towards those who wronged and abused him in his previous life. While the anime is very graphic, Keyaru's psychopathic methods of exacting revenge do not help the case of controversy for the anime.
3) How Not to Summon a Demon Lord- Diablo

To begin with, the series itself, the How Not to Summon a Demon Lord anime has several issues that lead to controversy. From fanservice to exploring concepts of slavery and age ambiguity, the series raised several eyebrows among anime fans.
Coming to the main character of the series, Diablo, while he may not be explicitly a "bad person", he has shown a tendency to assert dominance over others, especially the female characters. While the series has claimed to be an ecchi comedy, sometimes it hints at objectionable content.
4) Arifureta: From Commonplace to World's Strongest- Hajime Nagumo

Arifureta: From Commonplace to World's Strongest ended up on this list due to the main protagonist, Hajime Nagumo. The character arc development was highly unusual, in contrast to the standard Isekai genre anime series, prompting fans to take notice.
Before he was deceived, cast into the abyss, and abandoned to perish, Hajime was a shy and kind person. His fear of dying drove him insane and turned him into a heartless anti-hero. Following his metamorphosis, Hajime lost all morality and became vicious; his contentious behaviour demonstrated his total character shift.
5) The Rising of the Shield Hero- Naofumi Iwatani

While many readers might be confused about why The Rising of the Shield Hero anime series has made it to this list, there are some controversial aspects of the series that have not been addressed properly. From the very beginning, with the false assault accusation of Naofumi by Malty, the series treaded on a fine line of a very real life issue that is both sensitive and disturbing.
The accusation affected Naofumi's character. This made him lose trust in the opposite gender. The series also sheds light on the slavery aspect, and while Naofumi genuinely treats Raphtalia with care, the master-servant dynamic between them was never fully addressed in the series.
6) No Game No Life- Sora and Shiro

The No Game No Life series by Studio Madhouse has been criticized thoroughly by anime fans for multiple controversial angles. To begin with, the relationship between the main characters, Sora and his stepsister Shiro, has been portrayed as bordering on taboo territory.
Furthermore, the series is also filled with scenes of partial nudity and portrayals of minor characters in the wrong light. There are also some scenes in the anime that, despite being masked as comedic relief, feature unwanted or offensive issues.
7) Overlord- Ainz Ooal Gown aka Momonga

One of the most popular titles from Studio Madhouse, the Overlord anime series, has an extremely controversial narrative regarding the main protagonist, Ainz Ooal Gown, also known as Momonga. Unlike the natural trend in the genre, the main character here is a villain who kills, manipulates, and tortures others, without any signs of remorse.
Furthermore, the series also features a narrative of blind devotion from Ainz's followers, especially Albedo and Demiurge, often acting out of cruelty irrespective of whether Ainz ordered them or not. The series has mixed acts of cruelty and torture with comedy, raising some eyebrows.
8) Harem in the Labyrinth of Another World- Michio Kaga

The Harem in the Labyrinth of Another World anime series by Studio Passione has some of the most outrageous narratives when it comes to portraying slavery. The main protagonist, Michio, is isekai'd into a world where slavery and selling slaves are common practices.
The main protagonist even participates in the trade practice and starts building his harem. The series features nudity in multiple scenes, and is also very controversial when it comes to the exploration of concepts like slavery and consent.
9) I’m Standing on a Million Lives- Yusuke Yotsuya

Yusuke Yotsuya, the main protagonist of the I'm Standing on a Million Lives anime, has a dark temperament that comes to the fore throughout the series. He is a misanthrope who has no regard for human life. He only helps others when it benefits him or his cause.
The series also has a negative outlook for the female characters, creating a huge power gap between the female and male characters. Yusuke's insensitive comments towards them make it a controversial anime.
10) Tsukimichi: Moonlit Fantasy- Makoto Misumi

The Tsukimichi: Moonlit Fantasy series is one of the most protagonist-biased, controversial Isekai anime entries on this list. The main character, Makoto, has always been justified by the series, despite some of his unnecessarily extreme uses of force and questionable actions. The viewers could also sense the god-complex dynamic in Makoto's character.
Furthermore, the female characters share obsessive affection toward Makoto, with some of them having a significant age gap with him. There is also a power dynamic seen in the series, bridging the gap between Makoto and his companions, sometimes failing logical reasoning.
Final thoughts
The existence of controversial Isekai anime series cannot be avoided, due to the very nature of the genre, which heavily depends on one's imagination. However, there are some anime from the genre that cross certain boundaries, especially with their protagonists.
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