May Your Soul Rest in Magdala by Hasekura Isuna

Translated from Japanese Drama Fantasy Romance Adventure
It is a world in which order is maintained through three great factions: the Church, which bears the greatest authority; the Order of Clausius, possessing influence on par with the Church, claimant of immense assets and military might, and; the Guild of Commerce, an association of merchants and artisans alike.
In this world is the alchemist Kusla, who has been captured and imprisoned for the crime of burning a saint’s bones.
There’s been a spin-off novel announced with release on 10th January 2015 – Shoujo wa Shoka no Umi de Nemuru (少女は書架の海で眠る – A Girl Sleeps in the Ocean of Magdala).

Alternative names : Magdala de Nemure

1: Magdala de Nemure