The church seems to have been damaged as a result of measures taken to fortify Shrewsbury after the Parliamentarians took the town in 1645. On 2 December 1646 the Parliamentarian County Committee instigated a survey and set aside timber for repairs. In 1649 the churchwardens paid Thomas Landford £10 1s. to repair breaches on the north side and east end, using stones from the old abbey buildings, and were able to offset against this 3s. they made by selling materials recovered from the damaged part of the church. In this period the church was generally called Abbey Foregate Church, as Puritans rejected the veneration of saints and relics. Under the ultimately abortive proposals for a Presbyterian polity in Shropshire, dated 29 April 1647, Abbey Foregate parish was part of the county's first classis, along with most of the churches in Shrewsbury and the surrounding area. However, the minister was not appointed an elder of the classis and the parishioners remained uncooperative with Puritan church governance even after the collapse of the Presbyterian scheme.