The game is a sequel to the stage play YoRHa that was written by the game's director, Yoko Taro. The play takes place a millennia after the events of NieR and features a cast of female androids called YoRHa.

The collaboration between Square Enix and Platinum Games was agreed upon with the condition that Yoko Taro relocate from Tokyo to Osaka where Platinum Games was located. Although Taro was initially uneasy about the collaboration, the staff at Platinum Games had been wanting to work on a Nier game since its release, and their enthusiasm and wish to remain faithful to the original assuaged his doubts.

While designing the game's RPG elements, the staff at Platinum Games were at least partially inspired by The Witcher 3: Wild Hunt in the design of their sidequests, which they felt they would never be able to match. Game designer, Takahisa Taura, said:

"When we were making the game, The Witcher 3 came out. The sub-quest elements were so great, it was kind of demoralizing, so we just stopped playing the game..."

The game was written by Yoko, Haha Kikuchi and Yoshiho Akabane. The team defined the game's central theme as "agaku", a Japanese word meaning to struggle out of a bad situation. Another theme for the game was "love", which was unusual given that all the central cast were robots, which were not normally associated with emotions.

According to Yoko, while the scenario of Nier was "wet" in its emotional content, for Nier: Automata he aimed for a "dry" narrative concerning the world's inherent unfairness and the prejudices the characters are forced to confront.

The main framework of the game is themed around "uneasy children without parents" represented as "machine life-forms that have lost their creator" and "androids that have lost the humankind they were supposed to protect."

Much like the previous game being inspired by the September 11th and the War on Terror, Taro cites the changing political spectrum influencing the game. For example, changes from "reason to emotion" and "objective to subjective," which is represented by "President Trump being elected" and "the UK leaving the EU."

Pascal identifies as male but uses a female voice. The in-game reason is to soothe his adopted machine children. But in actuality, Yoko Taro claims that it is due to Takahisa Taura, game designer for Platinum Games, wanting voice actress Aoi Yuuki to play a role in the game.

The original plan was to make the game for mobile platforms or Play Station Vita. Yoko claims that they intended for it to be similar to farming simulator Farmville. But it was soon decided to develop the game for PS4 instead.

In Route C, if the player talks to Jackass after the bunker's destruction, she'll comment that she had a friend on The Bunker named "White." This friend is revealed to be The Commander in the Black Box Edition Art Book.