In designing the characters, Fujisaka used the previous two games' "Medieval Europe" inspiration for the enemies, while leaning towards more modern designs for the main characters.

Michael's prequel Novella suggests that he has met Angel and Legna, the playable dragons from Drakengard and Drakengrad 2. In the story, Michael dreams of his past companions, describing a red dragon who constantly watched his back and a black dragon who avoided conversing with him. Michael also exclaims that Red was about two thousand years older than him. The Red Dragon's official age in the first Drakengard is 10,000 year. This would make Michael 8,000 years old, despite his 12,000 year claim in the DLC.

The narrator, Partition, at the beginning of the game was a main support character from the prequel manga, Utahime Five. He was a magician who was well acquainted with the Lords of the Land and was able to use their life-stealing magic. When the Intoners came into power, all magic that sustained his youth was lost.

In early concept art, Accord is shown having a dragon or dragonic companion named Elma.

Kimihiko Fujisaka has said in a Famitsu interview that Zero's design was the first to be approved by Taro Yoko. He wanted more female characters to interact with her and asked Fujisaka to "think Puella Magi Madoka Magica" when designing them.

The scene in which Zero stabs Five to death was hinted to be so visually grotesque that it was censored in both Japanese and English versions of the game. However, the scene was aired uncut on the 7th NicoNico Live Broadcast.

The Disciple are named the "Apostles" in the Japanese release of the game. They were designed around prime male archetypes, and were given dialogue and personalities to contrast their appearance.

Aspects of Zero's design were incorporated into the designs of the other Intoners:
• One's outfit color scheme
• Two's flower as a design ornament
• Three's hairclip
• Four's armored left arm
• Five's shoulder decoration

Early concept art suggests that the centaur enemies were going to use bow and arrow weapons at one point.

One (Brother), is the great-great grandfather of the Seere and Manah in Drakengard.

Zero's original designs did not have the eye-flower. According to character designer, Kimihiko Fujisaka, he believes flowers are feminine and wanted to somehow include that for her design. He spontaneously plopped one into her eye for originality and to have her design stick out. Taro Yoko liked it as soon as he saw it and approved it for the final, despite the producer's hesitation for it.

Zero's crest has similar design features to Caim's Pact Mark from Drakengard.

Pop singer Eir Aoi was asked to sing "Kuroi Uta" for Drakengard 3, because she was said to be a fan of the Drakengard series.

Taro Yoko asked one of the main scenario writers, Sawako Natori, to have Mikhail "embody the good traits found in animals and children". Natori decided to borrow elements from fiction and strove to make Mikhail adorable. She had the most fun writing him.

A rejected idea for the game was to trick players into thinking that they missed a game from the series by calling it "Drag-On Dragoon 4", and have the story search for the "missing piece" of the series.

Another idea was to have the game set in a contemporary setting, following the adventures of a Japanese high school girl who calls for her dragon through her cellphone.

Takamasa Shiba presented the idea of creating a sequel to Drakengard 2 to Taro Yoko a number of years prior to the release of Drakengard 3. Yoko felt that he wasn't up to the task at the time and refused to work on the title. He was planning to continue expanding the NieR continuity, but his plans were cut short when ##Cavia## disbanded and Nier's producer, Yousuke Saito, became busy managing Dragon Quest X.

The weapon history of the "Eternal Wail" tells the story of how a sister who works in and tends to a library, and her twin who sings by a village fountain, protect the village and have done forever. This is a reference to Popola and Devola from NieR.

An unused weapon design from The Last Story was re-purposed as Two's Sword.