Atsushi Okubo's Soul Eater is an eccentric and interesting 2000s shonen that has an extremely unique feel due to its leaning into the occult, the spooky and the supernatural. The Halloween-esque atmosphere of the series, coupled together with good characters, are part of what make Soul Eater highly regarded as a series.
Like with most anime adaptations, the story is not quite 100% exactly the same as in the source material, since various elements in the production of anime itself have to be taken into account when it comes to having an adaptation. As such, its definitely worth it for fans to experience Soul Eater as an anime and as a manga, as there are some major areas in which they differ – here's how:
The Consumption of Souls
This is the biggest difference between the Soul Eater anime and manga, as it has some of the most profound effects on the ways in which both iterations of the series progress. In the manga, the conditions required for a Demon Weapon to evolve into a Death Scythe are that they must consume 99 evil human souls and the soul of a single witch. The only beings capable of doing so are the Demon Weapons, while in the anime, various other characters display the ability to consume souls. The 99 souls that Demon Weapons must consume appear on a list of targets laid out by Death himself, and this constitutes a regulation of who may or may not be hunted by Demon Weapons and their Meisters.
In the anime; however, this set of requirements is replaced with the Kishin Egg concept, where a Demon Weapon is required to consume 99 Kishin Eggs and the soul of one witch. In the anime, the Weapons and their Meisters track down Kishin Eggs using a techinque known as Soul Perception. Kishin Eggs are the corrupt souls of heinous criminals whose evil acts have begun to transform them into a Kishin, a threat powerful enough to bring about global destruction. In the Soul Eater manga, Kishin are borne from a Demon Weapon's over-consumption of pure souls, and the Kishin Egg concept simply does not exist.
The First Kishin
Due to the rule stipulating that Meisters cannot hunt down anyone who is not on Death's list in the manga, it features a much deeper origin and development of the Kishin concept than what is offered by the anime. For one, the threat of the Kishin is well understood by Death himself having defeated the individual who became the very first one in the series: Asura.
800 years prior to the events of the series, an individual engaged in a battle he thought he would lose committed the greatest taboo that could be committed by a Meister when he killed to gain power to overcome his fear of dying in the battle. He continued to secretly feed his Demon Weapon companion the souls of good people, eventually coming to be known as the first generation Kishin.
Asura was defeated by Death, who skinned him and sealed his body and soul in a sack made from his own skin; however, in order to fully contain the Kishin and the sheer amount of Madness he emitted, Death had to use his soul to seal Asura away. This limited Death's movement, and prompted his eventual establishment of Death City and the Death Weapon Meister Academy on that spot.
The whole reason why Death creates DWMA is to train young Meisters and Weapons and reinforce the number one rule that they only hunt the evil souls that Death himself has listed in order to prevent the birth of another Kishin. As such, the anime removes the point of Death doing any of those actions via the Kishin Egg concept, since Kishin Eggs are in effect the larval stage of Kishin in the anime.
The Death of Death
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In the manga, Asura is revived by the witch Medusa, and after his release from his prison, he engages in two battles against Death. In the second battle. Death and the DWMA engage Asura on the moon and Death loses his life as a result. Consequently, Death the Kid becomes the new Shinigami – God of Death. This does not happen in the anime because Death does not die in the anime-equivalent, but he is very badly wounded, which means that Death the Kid's arc is never completed in the Soul Eater anime.
He also does not have a second battle with Asura in the anime. Since Kid never becomes the Shinigami in the anime, he never gets to a point where he has the authority to make the huge decisions that he does at the end of the manga; such as forming a truce between the DWMA, as well as vowing never to make another Demon Weapon.
Mifune and Stars
Mifune, also known as the God of the Sword, is the mysterious samurai who protects the little witch Angela Leon, but is soon manipulated by Arachne into helping her cause. In the anime, he is the killer of Black Star's father, White Star; however, in the manga, the assassin was dispatched by the forces of the DWMA. In the climactic battle against the Arachnophobia organization, the anime and manga go in two different directions regarding the fate of Mifune. In the manga, Mifune is killed by Black Star, who subsequently abandons his assassin upbringing in favour of the way of the warrior, and Angela Leon is taken in by the academy. However, in the anime, Mifune is defeated but spared by Black Star, and is later allowed to become a teacher at DWMA. The anime Black Star also does not follow in Mifune's footsteps, but embarks on his own path which leads to his weapon, Tsubaki, gaining the ability to transform into the Red Uncanny Sword.
Crona
Crona is the unfortunate offspring of the Gorgon Medusa and the only weapon meister to the demon sword known as Ragnarök. Having been combined with their weapon partner by their mother, who aims to turn Crona into a Kishin. In the manga, Crona remains an antagonist in the series for much longer than they do in the Soul Eater anime. In the anime, Crona turns on Medusa but sustains serious injuries, and as such, the anime version of Crona does not kill their mother.
In the anime, Medusa's death comes as a result of Maka's use of the Demon Hunt technique. In the manga, Crona sacrifices themself to help Maka seal Asura away on the moon, but in the anime, it's implied that Crona lives on as a student at DWMA.