As the priory had been an Augustinian house, and therefore the church had both parochial and conventual functions, the nave was retained as a parish church. The choir, which had been solely for the use of the canons, was not spared however, and was demolished along with the cloisters, chapter house and associated buildings. The church remained this way until the Siege of Colchester in 1648 during the Second English Civil War. A Royalist army had seized the town, which was then surrounded and bombarded by the New Model Army led by Thomas Fairfax, with St Botolph's being caught in the crossfire of the assault on South Gate, reducing it to its present ruinous state.