Hinchingbrooke was sold to Sir Sidney Montagu on 20 June 1627. Sir Sydney was married to Paulina, daughter of John Pepys of Cottenham, great Aunt to Samuel Pepys. Their eldest son had drowned in the moat at Barnwell, which partly explains their move to Hinchingbrooke House.

Sir Sydney’s brother Edward was the first Lord Montague of Boughton Northamptonshire, and his other brother Henry was first Earl of Manchester with his seat at Kimbolton Castle.

The Montagues were an influential and powerful family.Sir Sidney Montagu was one of the Masters of Requests to Charles I and an ardent supporter of the royalist side in the Civil War. He died in 1644 and the estate passed to his son Edward Montagu, who carried out significant building works on Hinchingbrooke House.

Edward Montagu, fought on the Parliamentarian side during the first Civil War. Charles I slept at Hinchingbrooke in 1647 as a prisoner on his way from Holmby House to Newmarket. He was the prisoner of the radical Parliamentarian Cornet Joyce while Edward's wife Jemima entertained the king "magnificently and dutifully".

Despite fighting against the Royalists as a Colonel in Cromwell's army in the first Civil War Edward Montagu took no part in the second civil war and helped the restoration of Charles II to the throne - even collecting Charles from France when he made his return to England. On 12 July 1660 Edward was given the title Baron Montagu of St. Neots, Viscount Hinchinbrooke and Earl of Sandwich.

Having built Hinchingbrooke into a splendid country house he died at sea commanding a squadron of ships against the Dutch at Sole Bay near Southwold in 1672.
A picture of his ship in battle remains in the stained glass of the library window.
The left side shows Charles II's arrival at Dover, accompanied by Edward Montagu, to restore the monarchy.
The right side shows the death of Montagu, by then Earl of Sandwich, at the battle of Sole Bay.

The records the Montagu family history.
Edward Earl of Sandwich made considerable alterations here in 1661-64. The Earl was second cousin to Samuel Pepys and Pepys notes progress of rebuilding in his diary, visiting it in 1664.