During concepting phases, Kaine was at one point planned to be more elegant and dressed modestly, and she would wield one of the dropped tomes, Grimoire Schwarz. There were also concepts of a younger Kaine.

Originally, Emil's name was going to be "Snow" (as in Snow White.)

Early drafts of the game, Yonah's design shows that she was planned to grow into a mature age.

A version that combined elements from both versions, as well as new elements, was in development for PlayStation Vita. But it was canceled due to the development of Dragon Quest X taking precedence.

Nier was the only PlayStation 3 game Cavia finished before they were absorbed into Marvelous AQL.

There were originally thirteen Grimoires, but eventually all but three (Weiss, Noir and Rubrum) were cut from the game.

The combat was inspired by the God of War and Kingdom Hearts series, of which both Taro Yoko and Yosuke Saito were fans.

The creative director, Taro Yoko, has stated that much of the game's design were influenced by the September 11 attacks and the events that came after.

The development of Nier started after the release of Drakengard 2. The original concept was for a third entry in the Drakengard series. It was intended to be for seventh generation consoles due to the lessening importance of the PlayStation 2, which Drakengard 2 had been made for. However, as the project evolved, the original ideas were reworked and the game eventually became a spin-off from the main series. Despite this, the game's director Taro Yoko continues to think of it as the third Drakengard game.

The three DLC weapons are in the shape of the Red Dragon from Drakengard, each representing her evolutionary forms:
• Fool's Embrace is Level 1.
• Fool's Accord is Level 2.
• Fool's Lament is Level 3.

Many of the weapons in the game are weapons from the Drakengard series. At the end of the first Drakengard title, Spoiler:Caim dropped his weapons above Tokyo, where they were scatted, only to be found centuries later by Nier. They were later discovered and renamed:

• Moonfire became Moonrise
• Hymir's Finger/Broken Iron became Iron Will
• Battlelust became Captain's Holy Spear
• Ravenfeeder became Rebirth
• Dragonhook became Earth Wyrm's Claw
• Twins' Fang became Fang of the Twins
• Knight's Vow became Dragoon Lance
• Maiden's Kris became Nirvana Dagger
• Foul Blade became Vile Axe
• Kingsblood became Ancient Overlord
• Takamasa became Faith
• Skald's Song became Blade of Treachery
• Writheheart became Lily-Leaf Sword

In NieR Gestalt, the prologue takes place in 2049 with a 1,312 year time skip. In NieR RepliCant, the prologue takes place in 2053, and there is a 1,412 year time skip. It is unknown why this change was made.

The weapon, Kusanagi, takes its name from one of the Japanese Imperial Regalia, "Kusanagi no Tsurugi", but it is also known as "Ame no Murakumo".

One part of the game takes place in an old Mansion that features fixed camera angles. This area is a reference to the Resident Evil series.

Kaine is a hermaphrodite. In the artbook "Grimoire Nier", it states that due to ridicule for her being a hermaphrodite, "she had taken a liking to clothes that emphasize feminine characteristics", leading to her somewhat revealing attire.

The twins Devola and Popola get their name from the weapon "Devolapopola" (Skald's Song in the English release) from Drakengard.

Much of the game music's lyrics were written in "futuristic" versions of existing languages. For example the song "Kaine" was written in Gaelic, "The Wretched Automatons" in English and "Grandma" in French. Altogether the lyrics encompassed Scottish Gaelic, Portuguese, Spanish, Italian, French, English and Japanese.

When the Prince of Facade is rescued, he picks up the mask he was looking for in a manner much like Link in The Legend of Zelda series, including a jingle playing that is very similar to that of collecting an item in the Zelda series.

There are actually two versions of the game Nier. Nier: Gestalt (an Xbox 360 exclusive title) features an older version of the protagonist, while Nier: Replicant (a PS3 exclusive title) features a younger version. Originally the team had trouble deciding on what kind of protagonist they wanted for the game so they decided to make one game with an older protagonist to appeal to western audiences and a younger to appeal to Japanese audiences. Nier: Replicant was never released in the west.