The city records contain much information about repairs and alterations to the City Walls in the late-16th and early-17th centuries.

During the Civil War, York was the principal base of the Royal army assembled to fight the Scots. York withstood 11 weeks of siege by the Parliamentarians in 1644 and the Royalists only surrendered following defeat at Marston Moor. The City Walls were heavily damaged during the conflict. A temporary defence (sconce) built on the Mount to the southwest of Micklegate held out until the end of the siege. At St Mary’s Abbey, St Mary’s Tower was blown up, destroying many of the Abbey’s records.

All buildings between the Abbey and Bootham Bar were demolished by the Royalists, as part of their destruction of the suburbs to the north, west and east.

It was first contemplated that the walls could be used as a pleasure walk in the mid-17th century. The mid-18th century saw the transference of use from defensive to recreational purposes. A city charter meant the walls were kept in good repair during the late-17th and the 18th centuries.

During repair work (1736 to 1741) between Lendal and Monk Bar, consideration was given to providing a brick pavement, while new leases contained conditions which allowed walking on the walls.

The final time the walls were considered for use for military defensive purposes was during the last of the Jacobite rebellions. The walls were overhauled and repaired in 1745 in preparation but it was doubted that they would be strong enough to hold. However, the rebels retreated, returned to Scotland and were defeated at Culloden in April 1746.