During the reign of Elizabeth I, the Council of the North increased in importance and with it, York's revival and influence gathered momentum. The Abbot's lodging, now renamed King's Manor, was restored and both James I and Charles I stayed there during visits to York. Charles even set up the Royal Mint nearby and established his printing press in St. William's College. However, it soon became apparent that Civil War was inevitable and Charles left York in 1642.

Two years later, in April 1644, the Parliamentarians besieged York, but with the arrival of Charles' nephew, Prince Rupert, with an army of 15,000 men, the siege was lifted.

The retreating Parliamentarians were chased to Marston Moor, six miles from York. Unfortunately for Rupert, they turned on his army and he was devastatingly defeated. Rupert's army limped back to York and the siege was renewed.

But the city could not hold out for long, and on July 15 the Governor, Sir Thomas Glemham, surrendered to Sir Thomas Fairfax who gave orders to his troops that nothing was to be destroyed.