In 1603, Elizabeth died and James l became the first of the Stuart Kings. He was succeeded in 1625 by Charles l. During Charles reign, there were constant struggles between the Royalists and Parliamentarians. Northampton was primarily Parliamentarian in its support. The Battle of Nazeby in 1645 brought the defeat of the Royalists, and Charles was held for a while in Holdenby House.
It was during the civil war period, with the need for army footwear, that we first hear of Northampton picking up large contracts for boots.
In 1649 King Charles was executed and so began the eleven years of the Commonwealth rule. The Crown was restored in 1649 with the coronation of Charles ll, and in1662 he ordered the complete demolition of the remaining parts of the walls and the castle in order to prevent it from being used again as a Parliamentary stronghold.
On 20th September 1675 the Great Fire of Northampton broke out. Half the buildings were destroyed and many people left homeless. When news of the disaster spread, many towns and villages offered help, including a contribution of £11 1s 10d from Bugbrooke.
Meanwhile in Heyford the Parish Church acquired its bells. The first two in 1601, one of which was inscribed 'Thomas Morgan gave me to the Church, frank and free'. A third bell was added in 1638 and a fourth in 1704.
During the 1600s the Manor estates changed hands several times. Thomas Morgan passed them to his daughter, who married Sir John Preston of Furness in Lancashire. From him the estates passed to his brother Sir Thomas Preston. In 1685 he settled the manors of Heyford and Nether Heyford on his daughter Mary, who married William Lord Herbert, son and Heir of William, Earl of Powis. However, it is believed that the original Manor House building became derelict during this period. An entry in the Parish Registers of 1652 states that the building was unoccupied and 'lying open to vagrants'.
In 1674, William Bliss, a native of Heyford now living in Southwark and trading in wine, endowed, via his will, the village with a sum of £400 to purchase a School House (i.e. school room) and to pay for a School Master. The School was to be free to all children living in the Heyfords and also to any children by the name of Bliss living within 5 miles. The School eventually opened in 1683 with Rev. Gray as School Master.