The monastery was built on land given for the purpose in 1003 by Emperor Henry III to the Bishop of Halberstadt, and had been founded by 1009. In 1525 it was stormed, plundered and largely demolished by rebellious peasants; the monks were driven away, and did not return for several months.
The Vögte, or lords protectors, were the Counts of Wernigerode until 1429, when on their extinction their inheritance passed to the Counts of Stolberg, who at the Reformation were supporters of Lutheranism. From 1549 onwards the monastery was subjected to severe changes, and in 1555 it became, with its properties and assets, part of the territorial possessions of the Counts.
Part of the premises was used for a choral school, as in other monastic properties acquired by the Counts, and considerable re-building and improvements were made for the better accommodation of the function. The Counts' financial difficulties however caused the school to be suspended while the property was mortgaged, and although they regained it in 1608, and indeed lived there themselves for some years, the school finally closed in 1626.
Today, the abbey site and the adjacent Ilsenburg House are managed by the Ilsenburg Abbey Foundation (Stiftung Kloster Ilsenburg).