In the English Civil War he was first a Royalist captain and then in 1646 changed sides and joined the Parliamentary army.
He therefore, in March 1645, sent up his wife to inform the Committee of Both Kingdoms that he and Sir Trevor Williams undertook to deliver Monmouthshire and Glamorgan into Parliament's hands if they received adequate support.
[9] Various grievances existed at the time in the regiment, and the officers, knowing that Morgan could rely on the favour of Fairfax, asked him to forward a petition to the general.
[11] In 1651 Parliament granted him leave to stay in London for a few weeks to prosecute some chancery suits upon presenting a certificate that he had taken the engagement in Ireland;[12] and in 1652, upon his petition, they declared him capable of serving the Commonwealth, notwithstanding his former delinquency.
The next year Henry Cromwell requested him to assist Sir Timothy Tyrrell in arranging for the purchase of Archbishop Ussher's library.
[14] At the Restoration Charles II knighted him, 19 November 1660,[17] and appointed him commissioner of the English auxiliaries in the French army.
[20] Owing to political differences he lived on bad terms with his wife Elizabeth, who, being a staunch republican, objected to her husband turning loyalist.