In the place of today's church there was originally a convent of the sack brothers. This order was repealed in 1274 by decision of the Second Council of Lyon. In 1279, Bishop Heinrich von Isny gave the orphaned monastery to the Order of Clarissi, which has been documented in Basel since 1266. In 1320, the approximately 60-meter-long church comprised a hall-shaped long choir, the nuns' choir, of six pillar yokes with polygons. Adjacent to this was a three-aisled nave, which was about the same length, also known as the Leutkirche. The building had a flat roof throughout. The four western yokes that can be found in today's church come from this previous building.
In the wake of the Reformation, the nuns' choir was demolished in 1531 and a bulwark was built onto the nave in its place. From 1798 the Basel Catholics were granted hospitality rights in the church and in 1853 the long choir was given to the growing community. In 1858–1861 the church was enlarged.
City architect Amadeus Merian demolished the bulwark in 1858/1859 and doubled the old building to nine bays based on Gothic models, which ended in a short, polygonal vaulted choir. The nave and the choir were given a pointed roof and a roof turret with a bell sits enthroned on the church roof.