Many fans have speculated that Lucifel's appearance was based on the game's lead designer, Takeyasu Sawaki. In response to these claims, Sawaki has stated in an interview that Lucifel's appearance was based on American movies he saw, and was designed to make him look as human as possible. However, Sawaki does admit that some of their traits are similar.

El Shaddai was one of Ignition's two original IP's along with Dragon's Crown. However, when Ignition was acquired by Disney, El Shaddai was instead acquired by Takeyasu Sawaki's studio Crim.

After only one year, the game was re-released in Japan as an Xbox 360 exclusive, titled El Shaddai: Ascension Of The Metatron Encore Edition. The box art features Lucifel in place of Enoch.

Early Prototype footage shows that the game was originally titled Angelic Ascension of the Metatron. The footage also showed Enoch's armor having a sharper edge design, as well as the inclusion of combat with a sword and shield.

The game's aesthetic was inspired by popular anime, such as Neon Genesis Evangelion, Gundam, and works of Studio Ghibli.