A consecrated house of the Lord dedicated to the patron of the Roman Catholic Diocese of Chur, St. Lucius, is mentioned in documents as early as 1318. In the year 1370, talk is of a sister cell. The sisters lived according to the third order of St. Francis and were therefore referred to as Tertiaries. They dedicated themselves jointly to caring for the poor and sick.

Since at least 1328, the church has served as a parish church for Hechingen. With the consecration of the church of "Unserer lieben Frau und St. Jakob" in the upper town in 1488, the parish rights of St. Luzen Church were passed to it in practice, and the formal transfer took place in 1536.

The church was then neglected for decades until Prince Eitel Frederick I – the first ruler of the Hechingen Hohenzollern line – carried out the order left in the will of his great grandfather Eitel Frederick II. In 1586 he founded a Franciscan monastery and ordered a fundamental rebuild of the church. Today’s building, which was completed in 1589 and took the floor plan and parts of the external walls from its Gothic predecessor, embodies in the interior the striking colours of the late Renaissance.

Around 1700, the church was furnished in the baroque style in accordance with the changing tastes of the time. The hall was painted a uniform white and the altars were replaced. In the course of secularisation, the Franciscan monastery was abolished in 1808.

A comprehensive restoration project from 1971 to 1975 recreated the colour scheme of 1589.