After the inevitable surrender, two of the Royalist commanders, Lucas & Lisle, were executed by firing squad outside there castle. Colchester was left with its buildings in ruins, its cloth trade disrupted and it walls breached. The physical damage can still be seen in many places, including the ruins of St Botolph's Priory Church and the tower of St Mary at the Walls Church, both destroyed by cannon fire, the bullet holes in the Siege House and the large sections of the town wall later repaired in brick.
Less than twenty years after the Siege, Colchester was hit by the Great Plague. More than 4000 Colcestrians, over half the town's population died in the worst epidemic in modern England, but once again Colchester made a remarkable recovery from disaster.