On 21 October 1642 Morgan was knighted by Charles at Southam, Warwickshire, and two days later fought at the Battle of Edgehill. By the death of his half-brother, Colonel Thomas Morgan, who was killed at the Battle of Newbury 20 September 1643, he became possessed of the manors of Heyford and Clasthorpe, Northamptonshire; and had other property in Momouthshire, Warwickshire, and Westmoreland. He subsequently went abroad, but returned in 1648, when, though his estates were sequestered by the parliament by an ordinance dated 5 January 1646, he imprisoned several of his tenants in Banbury Castle for not paying their rent to him.