The second siege occurred on 29th February 1644, and was a more prolonged affair than the first. A force of 7000 men commanded by Major General Sir John Meldrum arrived and attacked the town. By the time of the second siege extensive defences had been built around the town, and the siege was far more of a battle of attrition than an assault. Cannons were fired into the town from sites on Beacon heights. One cannon ball knocked a hole in the spire of St Mary Magdalene Church, the damage is still visible from Mount Lane.

The house of Alderman Clay on the corner of the Market Place was also hit by cannon fire. The Alderman had previously dreamt on two occasions that his house would be destroyed and had moved his family and possessions out beforehand. To reflect his gratitude he left one hundred pounds to the local vicar on condition that he preached a commemorative sermon each year on the anniversary of the event. To this day the Hercules Clay Sermon is preached on the Sunday nearest to 11th March.

The Town was eventually relieved on the 21st March by 6000 men, 3000 on foot, 3000 on horse who arrived from Chester commanded by the King's nephew Prince Rupert. The Princes forces arrived in the early morning and took station on Beacon Heights. He ordered Colonel Tillier in charge of the Irish Regiments to move to Winthorpe in order to attack the Roundhead's flank. After a furious battle on the slopes of Beacon Heights Prince Rupert was victorious, and the roundheads surrended, handing over 11 cannon, 2 mortars and 3000 muskets.

The war itself was not going the Cavalier's way. After early setbacks the Parliamentary forces rebuilt themselves employing a form of military discipline among pikemen which hitherto had been lacking on both sides. A review of tactics was also associated with a strong puritan sense of purpose.

The New Model Army had reinvented an approach to warfare which proved decisive at Marston Moor on 2nd July 1644. With this the King lost control of the North. On 14th July 1945 Oliver Cromwell's Ironsides triumph at the Naseby. The Royalist Cause could not be retrieved after this, although the King would not concede defeat and the war is drawn out for almost another year.