Erfurt's Scottish Monastery and the associated Scottish Church were originally founded by Irish Benedictine monks in 1136. In the early 16th century, they were replaced by the Scots, who still give their name to the monastery and church today. In addition to their religious duties, they also devoted themselves to the sciences, taught at Erfurt University and held high academic offices.

The Scottish monastery was secularized in 1820. It was soon demolished, with only the church being spared.

Founded in 1136, begun in 1140 and completed in 1200, the three-aisled Romanesque first building of the Schottenkirche is no longer preserved in its original form after falling apart, reconstruction and restoration. The destroyed western Romanesque nave bay was replaced by early Gothic arcades in the early 13th century. The likewise Gothic choir was built after the second church fire in 1472.

Major renovations and extensions were carried out in the 18th century. These included the replacement of the solid vault with a wooden false vault due to defects in the masonry. The enlarged windows in the clerestory and side aisles also date from the same period. The baroque west façade was erected in 1727. On August 24, 1729, the church was finally consecrated by Auxiliary Bishop Christoph Ignatius von Gudenus.

In 1944 and 1945, shelling, incendiary bombs and air mines caused severe damage to the church. They also destroyed the organ, which was replaced by a new one in 1958. Extensive restoration work was carried out on the church and tower from 1956 to 1966 and again in 1979. Despite all this, the former monastery church is still recognizable today as a Romanesque basilica with three naves.