In the European release of the game, all the in-game tracks have unique names. The US release of the game simply uses generic names. For example, 'Track 1' in the US version is known as 'Marina' in the EU version.

The breast bouncing animations were toned down in the Playstation version, and the number of times the player can grab characters breasts was limited. According to the Playstation 20th anniversary Famitsu interview, the reason for this was because of a dispute between Hideo Kojima and SIE'S CEO Shuhei Yoshida, the latter believing that the feature was excessive.

Throughout the game, there are several NPC Revenants that are references to Team Ninja's works:

Shibasawa Kou - The game's producer
Samurai_Gaiden - Ninja Gaiden
Shadow Warrior - The European name of Ninja Gaiden
RebootRygar - Rygar
GITAROO-MAN - Gitaroo Man
theJaquio - The main villain from Ninja Gaiden
Holy_San - Holy Vigoor Emperor from Ninja Gaiden
Genshin07 - Genshin from Ninja Gaiden II
LOA.test.subject.1 - Lords of Alchemy from Ninja Gaiden 3
IreneIsMyHero - Irene Lew from the original Ninja Gaiden Trilogy
Dr. Smith - Dr. Walter Smith from Ninja Gaiden (NES)
oinin_AYANE - Ayane from Dead or Alive
nukenin_KASUMI - Kasumi from Dead or Alive
ZACK - Zack from Dead or Alive
GARI - Dr. Gari from Tecmo Secret of the Stars
KarmicPunishment - The curse from Ninja Gaiden 3
Hajinmon4Life - Ayane's fighting style, Hajin Mon
dropped_by_izuna - The Izuna Drop move from Ninja Gaiden and Dead or Alive

Nioh's story is based on James Clavell's 1975 novel Shōgun, which focuses on a fictional English samurai who examines the rise of a new Shogunate, based on the real-life William Adams.

The Dark Souls series was a major inspiration for the gameplay, as well as the team's older works, such as Ninja Gaiden and Onimusha. The loot system was also said to be inspired by Diablo.

The development of the game began in 2004 internally by Koei, four years before the merger with Tecmo in 2008. After it was scrapped, production was rebooted and transferred to Omega Force, and shifted the genre to something similar to Dynasty Warriors. This version was also scrapped.

Team Ninja was brought on to help develop the action gameplay in 2010, while earlier staff from the original Koei team handled the scenario, having a finalized concept in 2012. The final version was released in 2017, placing the project in development for between twelve and thirteen years.

The game was originally based on the unfinished Akira Kurosawa film, Oni. Though the idea was dropped in favor of an original story, the artistic elements and battle movements were inspired by other Kurosawa films such as Yojimbo and Seven Samurai.

One of the random peasants you can encounter in the game is Vitas Varnas, a reference to the actor, Did You Know Gaming? writer and Game Grumps contributor of the same name. Vitas is also credited in the game's credits under "The Noble Nobles".

The team originally wanted to give Dhalsim the ability to use the attacks 'Yoga Mummy' and 'Drill Kick' in reverse so that players could retreat. This feature was removed because the computer AI didn’t know how to handle it.

The team originally thought about giving Darun Mister the abilty to grow his moustache more and more with each victory, but the idea was never used.

In 2017, in celebration of Dragon Quest's 30th anniversary, a statue was erected in Sumoto on Awaji Island in Japan. Awaji Island is the birthplace of the series creator, Yuji Horii. According to Horii, each part of the statue is meant to represent something: the Slime for luck, the shield for protection from calamity, and the sword for to cut down evil fate.

The background of Green Hill Zone Act 2 was inspired by an early prototype version of Green Hill Zone from Sonic the Hedgehog.

The first batch of Nintendo Switch consoles suffered an issue where the left Joy-Con would frequently desync as the result of a manufacturing error. This could be remedied by placing a small square of conductive foam atop the Joy-Con's antenna traces, which would significantly reduce interference. Nintendo themselves would amend the desyncing issue in later batches of the Switch.

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."

Unused story mode rankings exist in the game's data for ranks D, E and F. In the final game, the lowest anyone can get in Story Mode is C.

Segata Sanshiro, a character that was created as part of an advertising campaign for the Sega Saturn, appears as an assist character in this game. He makes multiple references to the console, as well as a reference to one of his advertisements when partnered with Sakura and Gemini. He even references the different difficulty levels of the Fire Emblem series when partnered with Chrom and Lucina.

The vocals of some of the songs feature Vocaloids.

Hatsune Miku - "COSMO" and "It's A Wonderful World"
Megurine Luka - "Code 03", "Dragon Warrior", "Endless Journey", "Her Sword" and "LNS OP"
GUMI - "COMA" (composed by Vocaloid producer, ensou)

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 Ninja Hurk poster in Lilac's Treehouse was put in as nod to the Marvel character The Incredible Hulk, who Lilac's voice actress Dawn M. Bennet is a huge fan of.

The chanting heard in Act 1 of Relic Maze was done by Lilac's voice actress, Dawn M. Bennet.

The Japanese version states that the game takes place in the year 1999 on an altered earth that is stuck in a mythological medieval fantasy state. The western translation however, states that the game takes place in 13XX.