First mentioned as a Magdalene convent in 1241, St. Clara’s was affiliated with the order of the Poor Clares since 1279. Flourished around 1500; noted for its scriptorium and for its needlework (upkeep of the imperial robes). Noted abbess, Caritas Pirckheimer (1467–1532; sister of the humanist Willibald P.). During the Reformation, ban on new admissions. In 1591, the church became a Protestant parish church; the convent buildings served as the city pawn house. After 1806 the church was secularized. In 1854, it was granted to the Catholic congregation of the Frauenkirche as a filial church.

Richly carved Passion altar (1517), Crucifixion group by Veit Wirsberger (1510), Lady altar (ca 1500); in the choir, a Madonna of ca 1500; before the choir, tombstone and grave of Caritas Pirckheimer.

The convent was torn down in 1899. The church was partially destroyed by bombing on 16 March 1945 and was rebuilt 1948–1953.