He faced difficulties during the English Civil War: although regarded as a "puritanical preacher", he was questioned by the House of Commons on 19 March 1642 over allegations that he had criticized parliament and supported Charles I.
Even before that, he had been forced out of his position at St Stephen's Walbrook in 1641 and later forfeited the rectory of West Horsley for non-residence.
On the death of Thomas Westfield in 1644, Howell was appointed Bishop of Bristol by Charles I.
[3][4] His whereabouts thereafter until his death (between 20 March and 22 April 1650) are unknown, but his will left the lease of a property in Frogmore, Windsor to his ten youngest children.
He was buried in Bristol Cathedral after his death in 1650, his memorial stating Expergiscar ("I shall awake").