He remained inactive from politics until after the resignation of Richard Cromwell, when he was re-appointed to a position in the army in 1659. He prevented the sitting of the Rump Parliament and created a Committee of Safety with which to run the interim government. However, George Monck's march south caused Lambert's army to disintegrate and he was imprisoned in the Tower of London in March 1660. He made one final attempt to resist the Restoration of 1660 after escaping a month later, but his support had dwindled. He spent the remaining 24 years of his life imprisoned, first on Guernsey, and then on Drake's Island where he died in the winter of 1683–84.
Lambert, born at Calton Hall, Kirkby Malham, near Skipton in the West Riding of Yorkshire, of a long-established family, studied law at the Inns of Court in London. In 1639 he married Frances Lister, daughter of Sir William Lister.
In September 1642, Lambert was appointed a captain of horse in the Parliamentary army of the English Civil War, commanded by Ferdinando, Lord Fairfax. Within a year, he was colonel of a cavalry regiment, and distinguished himself at the siege of Hull in October 1643. Early in 1644 he did good service at the battles of Nantwich and Bradford. At Marston Moor (2 July 1644) Lambert's own regiment was routed by the charge of Goring's horse; but he cut his way through with a few troops and joined Oliver Cromwell on the other side of the field.
When the New Model Army formed in the beginning of 1645, Colonel Lambert was appointed to succeed Sir Thomas Fairfax in command of the northern forces, with the title of commissary-general. Fairfax was soon replaced by Sydnam Poyntz, and under this officer Lambert served in the Yorkshire campaign of 1645, receiving a wound before Pontefract. In 1646 he was given a regiment in the New Model, serving with Sir Thomas in the west of England, and he was a commissioner, with Cromwell and others, for the surrender of Oxford in the same year. "It is evident that he was from the first regarded as an officer of exceptional capacity and specially selected for semi-political employments".
When the quarrel between the Army and Parliament began, Lambert supported the Army's cause. He assisted Henry Ireton in drawing up the addresses and remonstrances issued by the Army, both men having had some experience in law. Early in August 1647 Lambert was sent by Fairfax as Major-General to take charge of the forces in the northern counties. His management of affairs in those parts is praised by Whitelocke. He suppressed a mutiny among his troops, kept strict discipline and hunted down the moss-troopers who infested the moorland country.