The Nunnery was rebuilt again after the Norman conquest, perhaps by AD 1100, by which time it was known as St Mary's Abbey.  In the sixteenth century it was one of the largest religious houses in England. There were 26 Nuns in a total establishment of 102 persons -  the latter including officials,  servants and children of lords and gentlemen who were there to be educated.

In November 1539 the Abbey was surrendered to Henry VIII as part of the Dissolution of the Monasteries and most of the monastic buildings were demolished. The site was subsequently gifted to the City by Queen Mary Tudor to celebrate her marriage to Philip of  Spain in the Cathedral in July 1554. The land was later divided into two, the eastern part was occupied by a fine town house and formal gardens that survive today as the Mayor of Winchester's official residence and public gardens. The western part of the site was cleared for the City's Guildhall in 1873. Between 1981-83 archaeological excavations were carried out on this site by the Archaeology Section of the Winchester Museums Service, revealing part of the Nunnaminster's fascinating history.

The earliest remains uncovered during the excavations were part of Ealhswith's Monastic church  Circa 903 (Marked in red). Most of it had been destroyed by foundations of the later churches that were cut through it. The surviving walls suggest that the church was built of timber, resting on stone foundations. The nave was about 6.5m wide with a grand double-apsidal ceremonial entrance at the West Front. A tomb found in the southern apse may be that of St. Edburga.  To the south of the church was a masonry base, perhaps for a monument or churchyard cross.

By 960 the Nunnaminster was said to be in a 'ruinous state'. As part of Bishop Ethelwold's reforms to the City's monasteries, the boundaries of the Nunnaminster were reorganised and the church rebuilt. Ethelwold's new church (Marked in red) was about the same size as Ealhswith's, but it was built of stone supported on broad foundations. inside the church was a feature thought to be a double tomb. To the South were the Cloisters, a feature apparently absent from the earlier monastery.