The Royalist army having disengaged and moved west, Browne was sent to capture Greenland House near Henley-on-Thames, under his original orders, and then moved to Reading. Ordered to join Waller at Abingdon-on-Thames, he objected that he had only 'three broken regiments of London auxiliaries, not above 800 in all' to hold Reading. In fact, he had fallen out with Waller and threatened to resign if forced to accept the latter's orders. In the end Waller left for London and Browne was put in command of the whole force at Abingdon, marching in with his brigade on 15 August. He and his troops were not involved in the Second Battle of Newbury in October, but as Governor of Abingdon, Browne kept up active skirmishing against the Royalist stronghold of Oxford during the winter. In the summer of 1645 he participated in the Second Siege of Oxford, and in September had to put down a serious clash between the garrison of Aylesbury and other Parliamentarian troops. He was again active in the final Third Siege of Oxford in 1646 and continued as Governor of Abingdon until the end of the First Civil War later that year.