On the outbreak of the English Civil War, he was appointed lieutenant-general of Shropshire, Cheshire, and North Wales, where he rendered useful military services, and was later made one of the Councillors of Prince Charles Stewart (who later became King Charles II of England), as well as a commissioner at the Treaty of Uxbridge in 1645.

He attended the Queen, Henrietta Maria of France (the wife of King Charles I), in her flight to France in 1646, but disapproved of her son Prince Charles's journey thither, and afterwards retired to Jersey; later, he subsequently aided in the King's escape to the Isle of Wight.

[3] Capell was one of the chief Royalist leaders in the second Civil War, but met with no success, and on 27 August 1648, together with Earl of Norwich, he surrendered to Lord Fairfax at Colchester, on the promise of quarter for life.

He succeeded in escaping from the Tower of London, wading the moat once he had got over the walls, only to be betrayed by a Thames waterman, who had been engaged to row him from a hiding place at the Temple to one in Lambeth.

[12] Capell wrote Daily Observations or Meditations: Divine, Morall, published with some of his letters in 1654, and reprinted, with a short life of the author, under the title Excellent Contemplations, in 1683.