Reynolds joined the parliamentary army, and was probably the Captain Reynolds whose gallantry is praised by Earl of Essex in his narrative of the surrender of the parliamentary army at Foy in September 1644. On the formation of the New Model Army he obtained command of a troop in Vermuyden's (afterwards Cromwell's) regiment of horse, and distinguished himself at the storming of Bridgewater. He is said to have taken a leading part in concerting opposition to the proposed disbanding of the army in 1647, and to have been for a time chairman of the committee of "agitators". Reynolds was popular with soldiers of advanced political views, and in 1648 was put in command of a regiment of horse consisting mainly of volunteer troops raised on the occasion of the Second Civil War, He was one of the officers in charge of King Charles I at Hurst Castle in December 1648. On 17 February 1649 his regiment was placed on the establishment, and ordered to be completed. It was intended to employ it in the relief of Ireland. Part of the regiment joined in the mutiny of the Levellers in May 1649, but Reynolds, with those who remained faithful, dispersed some of the mutineers at Banbury, held Newbridge against them, and joined in the final suppression of the revolt at Burford. The levellers denounced him in their pamphlets as an apostate and a traitor.