A manga adaptation, drawn by Tsunashima, was serialized in Dengeki Daioh starting on January 27, 2011, and published in Japan in a total of three tankōbon volumes.

Marii is enlisted into a secret organization that wants to take advantage of her powers, and becomes involved in a series of dangerous science experiments whose consequences ultimately force Gaku to make a difficult choice.

Farris described the early chapters of the story as "fun in an inoffensive way," and characterized it as deliberately light in tone in order to make readers more comfortable prior to its more serious plot developments.

While Farris said that he greatly enjoyed the story overall, he felt that the "dense" descriptions of theoretical quantum physics topics (which he said could necessitate frequent rereading for some), and some darker turns later in the narrative, could alienate certain readers.

[15] David Heath of Game Rant included Qualia in a list of "best" science fiction light novels that did not yet have an anime adaptation.