On the outbreak of the Civil War, he raised two regiments, one of horse and the other of foot, composed chiefly of Roman Catholics, for the service of the king, forming part of the Lancashire forces under the command of James Stanley, 7th Earl of Derby.
After the surprise capture of Wakefield on 21 May 1643, the Earl of Derby being then with Queen Henrietta Maria at York, Molyneux was ordered to conduct the Lancashire forces thither.
He was defeated on 20 August 1644 by Major-general Sir John Meldrum at the battle of Ormskirk, and narrowly escaped capture by hiding in a field of corn.
On 30 June 1648, a warrant was signed by the Derby House Committee for his arrest, as having, contrary to an ordinance of Parliament, approached within twenty miles of London.
[3] Molyneux joined Charles II on his march to Worcester, and escaped after the battle on 3 September 1651, but died shortly afterwards, probably in 1654.