Montagu played no part in the Second English Civil War and retired from Parliament after Pride's Purge in December 1648 to live quietly at home. He returned to politics in 1653 when his neighbour Oliver Cromwell nominated him to the Barebones Parliament as MP for Huntingdonshire, a seat formerly held by his father who died in September 1644. He was also appointed to the English Council of State, an office he held until it was dissolved in 1659, and was re-elected to the First Protectorate Parliament in 1654, then the Second Protectorate Parliament in 1656.