In 1608 he was presented to the rectory of Foxcott in Buckinghamshire by Henry Wriothesley, 3rd Earl of Southampton, and afterwards became lecturer at St. Peter's in Cheapside and at St. Paul's Cathedral for five years.
On 11 January 1611–12 he was instituted rector of St Benet Sherehog in London through the influence of his patron, John Williams, and resigned the rectory of Foxcott.
He had strong high-church sympathies, which roused the dislike of the puritans, and after the appearance of his first publication, The Resolution of Pilate, they prevailed on John King, bishop of London, to suspend him in 1616.
After his suspension, from which he was eventually released on appeal to the prerogative court, he resigned his living, retired for a short time to Cambridge, and, on his return to London, found friends in the archbishop of Canterbury, George Abbot, and in the chancellor, Sir Thomas Egerton, who presented him to the rectory of Llanllechid in Carnarvonshire.
He was on the point of being nominated tutor to Prince Charles and the Duke of Gloucester, but at the last moment William Laud, who disliked him in spite of their theological sympathies, obtained the appointment of Brian Duppa instead.
Williams also states that "before he was forty years old, he narrowly escaped being elected bishop of St. Asaph," probably on the death of John Hanmer, but on that occasion also saw another preferred to him at the instance of Laud.
The sheets were actually in the hands of Sir John North, one of the commissioners, but Williams contrived to get it from him before he had looked at the title, and afterwards, by representing himself as a victim of the Irish rebels, he procured a safe-conduct and the restitution of his belongings.
Early in 1643 he published his Vindiciæ Regum, or the Grand Rebellion; that is a Looking-glass for Rebels, whereby they may see, how by Ten Several Degrees they shall ascend to the Heighth [sic] of their Design (Oxford, 4to).
On 8 March 1643/44, while he was preaching at the university church before the royalist parliament, his house at Apethorpe was plundered by the parliamentary troops, his wife and children driven forth, and his possessions sequestered.
His sufferings increased his zeal, and in the following winter appeared Jura Majestatis; the Rights of Kings both in Church and State, granted first by God, secondly, violated by Rebels, and, thirdly, vindicated by the Truth; and the Wickedness of the Faction of this pretended Parliament at Westminster (Oxford, 1644, 4to).
After in vain exhorting the royalists to resist, he managed by a succession of adroit stratagems to reach Ireland, and on 1 April 1647 was presented to the rectory of Rathfarnham, near Dublin.
Ormonde sent him a sum of money to relieve his necessities, but on his way to Wales, to live on a small patrimony he possessed there, he was taken prisoner by Captain Beeche, who robbed him of all he had and left him to make his way back to Dublin in a destitute condition.
On repairing to his diocese he found his palace and cathedral in ruins, and was immediately involved in numerous lawsuits in his endeavours to recover the alienated lands of the see, in which he was generally unsuccessful.
In 1664 he published The Persecution and Oppression of John Bale, Bishop of Ossory, and of Griffith Williams, that was called to the same Bishopric (London, 4to), an animated autobiography, to which he appended a description of the distressed condition of the clergy of his diocese.