Director Masayuki Kojima was asked in April 2015 by producer Muneki Ogasawara of Kinema Citrus to direct the project, and he agreed after reading the original manga and finding it fascinating.

Character designer Kazuya Kise was chosen on Kinema Citrus's suggestion; director Kojima found it refreshing that Kise, known for a stylish art style, could draw such cute characters, and manga author Akihito Tsukushi praised Kise's skill at drawing adults.

Manga author Akihito Tsukushi disliked the first chapter of his original manga, so during production meetings he asked the anime team to keep the opening as short and polished as possible, which resulted in a high-quality adaptation.

For episode 10 of the TV series, where Riko's arm breaks, voice actresses Miyu Tomita (Riko) and Marina Ise (Reg) coincidentally both looked at images of broken bones to prepare for their performances.

The score was composed by Australian composer Kevin Penkin, and recording sessions were held in Vienna, which a writer noted gave the soundtrack an exceptional quality unusual for Japanese anime.

For the film 'Made in Abyss: Dawn of the Deep Soul', Miyu Tomita was given the difficult direction to keep the emotional feel of Riko's crying while removing the raspy throat sound that would be noticeable in theater sound systems.

For the same film, Shiori Izawa (Nanachi) found it easier to build feelings of fear and hatred because she was able to record her lines in the same session as Tomoyuki Morikawa, who voices Bondrewd, unlike in the TV series where she had to imagine the antagonist's presence alone.

The film 'Dawn of the Deep Soul' was initially rated PG12, but the Japanese film classification board raised it to R15+ at final review, forcing the production committee to offer ticket refunds to under-15 viewers who had already bought advance tickets.

The short anime 'Marulk-chan's Daily Life', shown as a bonus before screenings of 'Dawn of the Deep Soul', was based on an illustration originally used as an April Fools' joke in 2019 claiming the main film would be replaced by this short.