The planning began in 2015 when director Kyogoku Takahito was producing Gate, and it was triggered by Toho's Takei Katsuhiro proposing the adaptation of Land of the Lustrous. Director Kyogoku had long wanted to create anime combining 3D as a base with 2D, and he and Takei agreed that this style would suit this work.

Takei Katsuhiro had wanted to entrust this work to Orange from the start. While director Kyogoku trusted Orange's abilities from his action production experience on Evangelion: 3.0 You Can (Not) Redo, he was concerned about the small number of staff members, but during production the studio expanded from 50 to 100 people.

In typical anime, voice recording is done after the visuals are completed, but in this work, an unusual order was taken where voice actor recording was done before CG production, after animatics were created.

Director Kyogoku states that after hearing the performance of Kurosawa Tomoyo, who voices Phosphophyllite, the character portrait of Phos that he had struggled to grasp became clear. He explains that the 300 years spent doing nothing created a throwaway attitude, and even when angry, she couldn't fully commit—Kurosawa's acting embodied this difficult personality with exquisite ambiguity.

Regarding the role of Kongou, director Kyogoku stated that he was particularly satisfied to be able to cast Nakano Yutaka, with whom he had prior experience working together and whose acting he appreciated. He also noted that a voice too charming or suggestive would not have suited the character of Kongou.

Because it was difficult to express the translucent texture of gems through hand-drawn animation, the decision was made to base the work on CG animation. From the beginning, director Kyogoku had conceptualized the characters as figures with clearly articulated movable parts.

The work of concept artist Nishikawa Yoichi greatly influenced director Kyogoku's vision, and many cuts in the film are directly based on Nishikawa's drawings. In particular, director Kyogoku states that one piece depicting Phos's realistic hair colored in cel shading placed behind CG grass had a significant influence.

Cinnabar, surrounded by mercury and requiring delicate acting and fine hair expression, was a particularly challenging character in animation production.

2D animation was produced as "guide animation" to direct the 3D animation, and one of those in charge was Matsumoto Norio, known for action animation on Naruto.

In the English translation, on the instruction of original author Ichikawa Itsuka, singular "they" was used as a gender-neutral pronoun to depict characters as genderless beings. In the Japanese script, a pronoun closer to "kare" (he) is used, but it is said to carry a more ambiguous nuance.

This work was evaluated as a turning point for CG anime, earning high praise as a work that even viewers skeptical of CG anime found convincing, and it is counted as one of the representative anime of the 2010s.

The package design for video software in Japan was handled by book designer Yamada Tomoko, for whom this was her first work related to anime, with a design inspired by a jewel box.