Morgan fought in the Low Countries and in particular assisted the Dutch in the decisive victory at the battle of the Slaak in 1631. He fought under Fairfax in the English Civil War. In 1645 he was appointed parliamentary governor of Gloucester.
In 1646 he took Chepstow Castle and Monmouth, and besieged Raglan Castle.
From 1651 to 1657 he assisted General George Monck in Scotland and was promoted to major-general. He was second in command in Flanders in 1657 and knighted on his return in 1658.
He rejoined Monck in Scotland, and played a conspicuous part in the Restoration in Edinburgh. He was appointed Governor of Jersey in 1665 repairing the Jersey forts and reorganising the militia.
A pamphlet narrating his acts in France and Flanders in 1657 and 1658, said to be by himself was published in 1699.