Charles created him a baronet in recognition of his services, but his capture during the English Civil War led to his estate being sequestered.
Morgan was one of the Morgan family of Llantarnam in Monmouthshire, Wales, an established Roman Catholic family: his great-grandfather William Morgan was a Member of Parliament in the reigns not only of the Catholic Queen Mary but also of the Protestant Queen Elizabeth, and allowed his house to be used for the celebration of mass.
He was educated at Jesus College, Oxford, matriculating in 1616 and obtaining his Bachelor of Arts degree in 1619.
He was involved in the Welsh Jesuit headquarters being set up in 1635 in Cwm, Llanrothal, Herefordshire.
He was commissioned in the second Bishops' War in 1640 and given permission to obtain contributions from fellow Catholics.