From 1636 he was Colonel of the Pickering Lythe Trained Band and commanded it during the First Bishops' War.[3] During the years when Charles I ruled without Parliament, Cholmeley became, together with Sir John Hotham, one of the leaders of resistance among the Yorkshiregentry. He organised a number of petitions and protests, and in 1639 he refused to pay ship money. As a result, he was dismissed from all his posts and was summoned before the Council of State, the King reportedly telling Hotham and Cholmeley that if they interfered again he would hang them both.[4]
In April 1640 Cholmeley was again elected a member for Scarborough in the Short Parliament. He was re-elected for Scarborough for the Long Parliament in November 1640 and was created a baronet in 1641.[5]
Initially, a Parliamentarian when the civil war broke out, Cholmeley was one of the parliamentary commissioners sent to negotiate with the King in May 1642; he raised a regiment for the Parliamentary army which fought at the Battle of Edgehill and later joined Fairfax in his campaign against the royalist garrison at York. However, when the Queen landed in Yorkshire, returning from the Netherlands where she had been attempting to raise money and troops, Cholmeley declared for the King, and Newcastle put him in command of all maritime affairs along the northern half of the Yorkshire coast. He was disabled from sitting in parliament in 1643. After the Royalist defeat at the Battle of Marston Moor, Cholmeley refused to flee the country, holding Scarborough for the king during its Great Siege, until he was forced to surrender, on very favourable terms, on 22 July 1645.[4] His estates were sequestrated, but he later compounded for £850.
Cholmeley spend time in exile, until returning to England in 1649. He wrote his memoirs before his death on 30 November 1657. It was addressed to his sons, and intended to "embalm the great virtues and perfections of their mother", who had died two years earlier.[4]
D. Brunton & D. H. Pennington, Members of the Long Parliament (London: George Allen & Unwin, 1954)
J. Foster, Pedigrees of the County Families of Yorkshire
Major Robert Bell Turton, The History of the North York Militia, now known as the Fourth Battalion Alexandra Princess of Wales's Own (Yorkshire Regiment), Leeds: Whitehead, 1907/Stockton-on-Tees: Patrick & Shotton, 1973, ISBN 0-903169-07-X.