The idea for an anime adaptation of Nier Automata was proposed by Aniplex in 2017, shortly after the game's release; Yoko Taro was surprised since anime adaptations are usually made as tie-ins to boost sales rather than years later.

Yoko Taro initially clashed with director Ryōji Masuyama and Aniplex over how faithful the anime should be to the game, arguing that simply replicating the game's story would be boring, which led to a prolonged debate before agreeing to mix faithful sections with anime-original content.

Yoko Taro deliberately kept some creative distance from the day-to-day writing to give the anime team freedom, while still adding new material such as deeper exploration of A2's backstory that wasn't obvious in the game.

Actor Natsuki Hanae was present at an early planning discussion between Yoko Taro and game producer Yosuke Saito and reacted with disbelief upon learning an anime adaptation was being made.

Yoko Taro personally voiced cameo roles as two different Machine Lifeform characters in the series.

A-1 Pictures received the game's original CG character models from Square Enix and built key frame animations for common expressions, sometimes simplifying clothing designs and movement to make animation more manageable.

The black-and-white looking Bunker scenes and opening animation were difficult for the art team, who had to find a shade of color close enough to convincingly mimic a monochrome effect.

Each episode ends with a short puppet show created by Moge, with puppet designs for the YoRHa characters based on patterns from the full-sized character designs.

Composer Keiichi Okabe was told he could freely use and rearrange the original game's score, which reassured him given the high expectations surrounding the anime adaptation.

Amazarashi, who previously worked with Yoko Taro on a promotional song for the game, wrote the first cours' ending theme 'Antinomy' around the narrative's theme of uncovering truths opposite to one's beliefs, and Yoko directed a special music video for it featuring a puppet show retelling the game's story using Machine Lifeforms.

The second cours' ending theme 'Ai to Inori' was composed by Keiichi Okabe with lyrics written by Yoko Taro himself, performed by virtual idol group Gems Company.

The broadcast of the first cours was delayed twice due to production issues caused by a resurgence of the COVID-19 pandemic, with episodes 9-12 eventually airing back to back on July 23.

Collider praised how the second season handled A2's character, arguing her portrayal in the anime surpasses that of the original game.