The church's origins lie in a Benedictine nunnery founded around the mid-1100s under Archbishop Eskil, dedicated to the Virgin Mary and St Peter. The earliest documented reference to the convent dates from about 1164. The original building was constructed in the Romanesque style of the period, using sandstone with rounded arches, comparable to the style still seen at Lund Cathedral.
By the 1300s the growing congregation required a larger building, and the church was rebuilt in red brick in the Gothic style, replacing the earlier Romanesque structure. It has been described as one of the purest and noblest examples of medieval Gothic brick churches, though such praise should be read as a matter of opinion rather than settled fact.
When the Reformation swept through the Nordic region in the 1500s, most of Lund's medieval monastic buildings were demolished and their properties passed to the crown. The convent buildings themselves were pulled down around 1600, but the church survived, apparently because it also served as a parish church. Alongside Lund Cathedral, it is the only medieval church in Lund to have survived this period of destruction.
The building suffered further damage during the wars between Denmark and Sweden, and by 1653 it was said to be almost entirely destroyed, though it was later restored. A thorough restoration in the 1920s aimed to return the church to something closer to its original medieval appearance, and included new mural paintings by Olle Hjortzberg.
None of the church's original medieval furnishings have survived. A carved altarpiece triptych, made in Germany in the 1400s, was brought into the church in 1931, and the pulpit dates from the early 1600s. The mechanical organ in use today was built in 1959 by the Danish firm Marcussen & Søn, replacing an earlier instrument by the same maker from 1936.
The adjoining churchyard is the resting place of a number of prominent figures connected with Lund University over the centuries, alongside other notable burials, giving the site a continuing connection to the city's academic and civic history.