Halifax Parish Church witnessed further upheavals during the English Civil Wars of the seventeenth century, a period of bitter conflict, which caused severe disruption to the local textile trade. A Puritan stronghold, Halifax suffered occupation by both Royalist troops after the Royalist victory at Adwalton Moor in 1643 and by Parliamentarian forces after the Royalist defeat at Marston Moor.
Dr John Favour’s energetic and inspiring ministry as Vicar of Halifax from 1593 to 1623 promoted the growth of Puritanism in the parish and an upsurge in charitable bequests including the endowment of Heath Grammar School. Favour’s Puritan successors, included Dr Robert Clay, Vicar of Halifax from 1624-28, who converted the charnel house in the crypt in 1626 into a parochial chained library, whose collection of rare books is now housed in the University of York.
However, the Laudian Vicar, Dr Richard Marsh appointed in 1638, sought to restore the liturgical practice of the Pre-Reformation Church, arousing the opposition of the Puritan laity. He fled on the outbreak of the Civil War to join the royalist forces, but was taken prisoner at Manchester and the revenues of the vicarage helped to finance the forces of Lord Ferdinando Fairfax.
The Puritan stronghold of Halifax suffered a Royalist army of occupation after the Royalist victory at Adwalton Moor in June 1643, but the town reverted to Parliamentarian control early in the following year, which ended with the Restoration of the monarchy in 1660.
However, a native of the parish of Halifax of Puritan descent, Dr John Tillotson, later preached the thanksgiving sermon for the accession of William and Mary after the Glorious Revolution of 1688 and was subsequently appointed Archbishop of Canterbury and the remains of the influential Dissenting preacher, Oliver Heywood were interred in the Parish Church in 1702.