The convent originated from a community of Beguines at S. Ulrich in Weihengau. Circa 1270 the community moved to Lauingen and developed into the Cistercian abbey of S. Agnes. By 1284 the women were placed under the spiritual supervision of the abbot of Kaisheim, and in 1319 they were formally incorporated into the Cistercian order. The convent's admittance to the order, with all its freedoms and privileges, was reaffirmed by the General Chapter in 1459. The female leader of the convent, previously referred to as the magistra, was now given the title of prioress(Krausen, 69). In 1475 the nuns received the right to elect their own chaplains, mostly drawn from members of Kaisheim.

Outside of the city, the convent held no rights and few possessions, only a few small farms and fields. Any acquisitions of the convent within the city involved the city council and overlords.

The archives for the community are found in the Hauptstaatsarchiv in München (Munich)as well as in the Staatarchiv Neuburg and the Stadtarchiv Lauingen.

Circa 1489 prioress Agnes Haydin lead a reform of the convent. The Reformation brought difficulties for the convent. In 1542/1562 the nuns were forced from the convent and had to flee the city. They were taken in by the Dominican convent "Auf Hof" near Neidingen. The nuns of Luaingen formed their own 'community' within the convent. S. Agnes was dissolved for the first time and a school for Protestant theologians was established in the cloister buildings. In 1643 the Cistercians returned to the cloister, and in 1671 the community was raised to an abbey. Final dissolution of the convent occurred in 1803 (Krausen, 70).