As a member of the House of Lords, Lindsey remained a loyal supporter of the King. The Lord Parliament withdrew his commission as lord-lieutenant of Lincolnshire in February 1642, after which he joined the King at York. He was appointed commissioner of array for Lincolnshire in July and lord-general of the King's army in August.
When Prince Rupert was appointed commander of the Royalist cavalry, he was exempted from taking orders from anyone but the King himself. This placed Lindsey in a difficult position and led to bitter acrimony. At the council of war before the Battle of Edgehill in October 1642, Lindsey quarrelled with Rupert and the King's field marshall Lord Forth over the deployment of troops. When the King followed Forth's advice, Lindsey angrily resigned his commission and Forth replaced him as general-in-chief. During the ensuing battle, Lindsey fought on foot as a colonel at the head of his regiment. He was wounded by a shot in the thigh and taken prisoner by the Roundheads. Carried to a nearby barn, he died from his wounds the following day.