By 1619 Moyse's Hall was owned by a gentleman called Henry Collinge and in 1626 it was sold to the Guildhall Feoffment Trust. This Trust was a charity, originally established by the medieval Candlemas Guild, which administered a number of charitable bequests made to the town. After the dissolution of the abbey, the Trust assumed an important role in the governing and maintenance of the town. The Feoffees used Moyse's Hall as the town gaol, the workhouse and the bridewell, or house of correction. It housed both poor people and offenders.

The Feoffees kept good records of their properties and a number of documents survive from the 17th and 18th centuries describing the items bought for the inhabitants, the people appointed as keepers and the repairs made to the building. Shoes and stockings were bought for the inmates and woollen cloth for their clothes. These included 'shyftes', 'a petycote', 'a wastecote', 'a dublette and hose', 'a shirte', 'a curtll and wastecote', ,aprons', 'smocks', and 'necke clothes'. Rye straw was bought for their beds and linen cloth for sheets. Tools were bought for their work of preparing hemp. Some food was bought, such as bread and beer, but not a great deal: one account notes sadly 'ii s to buy breade, they had noe worke that day beinge Saterdaye nor nothinge to eat upone Sundaye'

By the 1730s, the number of inhabitants was apparently too great for one building, and the workhouse was moved elsewhere. After this Moyse's Hall was generally referred to as the Bridewell. There was another prison on the, west side of Cornhill which had been used by the Abbot before the Dissolution. It continued to be used as a prison until 1804 when a new gaol on Sicklesmere Road was opened. It appears that serious offenders were housed in the prison, whilst more minor offenders (vagrants, drunkards, prostitutes, etc.) were sent to Moyse's Hall. Clearly, however, Moyse's Hall was not as well-used as formerly, for the Guildhall Feoffees sold off some parts of the building in 1812. In 1836 a police force was established in Bury St Edmunds, and Moyse's Hall became the police station. Even then, part of it was still used to house offenders.

In 1791 a proposal was made, to erect a turret clock on the top of Moyse's Hall. It was a handsome structure with a cupola and is shown in some early prints. In 1858, considerable restoration work was carried out to designs by George Gilbert Scott, the then fashionable Victorian architect who designed the Albert Memorial in London. Many features of the building can be dated to this restoration: in particular the clock turret with its cupola was taken down and replaced by the turret that survives today.