On the city’s plague cemetery St. Petri was erected in place of a chapel that had seriously fallen into disrepair by 1295. Construction work for the new church began around 1352. A few years later, in 1356, the church is first mentioned as completed. She belonged to the parish of the Teutonic Order that was based in Mühlhausen’s new town. The first agreements regarding the liturgical care are dated 1371. St. Petri Church became an independent parish  only in modern times. The late-Gothic building with its five-sided apse has seen several changes. After the nave’s arching ceiling had collapsed during a city fire in 1422 it was replaced by a flat ceiling. Rubble from the abandoned St. John’s Chapel at the Blobach square were used to build a new entrance hall in 1577. Between 1893 and 1895 St. Petri received its present shape when the nave’s arched ceiling was restored and extended towards the west, and the façade was renewed.

 In 1927 the parish of St. Petri had a memorial chapel built into the northeast aisle, dedicated to the victims of the First World War. The commemorative plate containing the names of the fallen was designed by stonemasons of the local Carl Schilling. The sculptor Walter Krause (1891-1967) from Mühlhausen was commissioned to design the monument in front; he also created the rather famous figure of the “Indignant Christ”. The Lord and Saviour is represented devoid of iconographic attributes of divinity, as a simple human being that is taken aback by the senseless mass killings. The sculpture is somewhat contrasted by the text on the memorial plate reading, “How did the heroes fall and the quarrelsome die?”. a line that also appears in Krause’s own work, quoting the Lord’s Prayer on the pedestal: „Your will be done“. The hero worship as a mans of coping with the trauma of the First World War during the Weimar Republic is in stark contrast to the design of the memorial chapel within the church. The motif of the rebelling Saviour for this monument has received attention beyond Mühlhausen even before it was built. For instance, Käthe Kollwitz (1867-1945) wrote to Walter Krause: “The idea to depict an indignant Christ to mourn the fallen in a church is beautiful and brave […]. All those who have suffered from war will understand you.“