Originally, the Fuggerei did not have its own place of worship. Residents visited the nearby St. Jakob Church. During the Reformation, however, that church became Protestant. The Catholic Fuggers responded and built a new church on the Fuggerei grounds: By order of the administrators Markus and Philipp Eduard Fugger, construction began in 1580, probably led by the master builder Hans Holl. The result was a simple church, which was dedicated to Markus the Evangelist in 1582. A distinctive architectural feature: In contrast to most Catholic churches, St. Markus was not built facing eastward; rather, its orientation was determined by the direction of the street on which it was built.
Until construction of the Heilig-Grab Chapel in 1613 (now St. Maximilian), St. Markus was the only Catholic church in the area. Here, the Catholic Fuggerei residents could celebrate Mass. The church has room for approximately 200 people.
St. Markus was reconstructed during the baroque era and was newly furnished. During the bombing raid of February 1944, the entire church interior burned. In 1950, it was rebuilt and furnished with salvaged or newly provided elements. As a result, St. Markus still has some interesting artworks such as the altarpiece with a crucifix by Jacopo Palma il Giovane (circa 1595) and the original epitaph for Ulrich Fugger from St. Anna, which was made by Adolf Daucher, probably based on designs by Dürer. Built between 1550 and 1560, the coffered ceiling, with its notable marquetry, is probably from the Fugger Foundation House near St. Anna.