He returned to Wales, and, after acting as tutor in a family for a year and a half, became curate of Withycombe, Somerset, under one Jones, vicar of Taunton.
Subsequently, he served the Bishop of Vicenza, and visited Milan, and was admitted to the English seminary at Rome.
He appears to have voluntarily presented himself before the inquisition, 27 April 1578, and was commanded to preach in defence of the Roman church before the pope and four cardinals on 25 May 1578.
Nicholls remained at the seminary two years, but professed to despise the scholars who, he says, could ‘neither construe Latin nor preach as well as the shoemakers and tailors in England.’ Having obtained from the pope a viaticum of fifty crowns, under pretence of ill-health he left Rome some time in 1580 for Rheims, where Allen was then living.
During his imprisonment he wrote: ‘John Niccols Pilgrimage, wherein is displayed the lives of the proude Popes, ambitious Cardinals,’ &c., London, 1581; also ‘A Declaration of the Recantation of John Nichols (for the space almost of two yeeres the Pope's Scholar in the English Seminarie or Colledge at Rome), which desireth to be reconciled and received as a member into the true church of Christ in England,’ London, 1581.
It was answered by Thomas Lupton in ‘The Christian against the Jesuite, Wherein the secrete or namelesse writer of a pernitious booke intituled A Discouerie, &c. … is … justly reprooued,’ London, 1582.
Upon Easter Sunday, 19 March 1581, he preached there before a large company of nobles and courtiers invited by Sir Owen Hopton (Records of the Society of Jesus, ii.
But at the end of 1582 Nicholls again crossed to the Low Countries and Germany, in company with Lawrence Caddey, his former fellow-student at Rome, who had also recanted in England.
On 20 February 1583, Nicholls was examined, and retracted his accusations against the English colleges at Rome and Rheims, to which Dr. Allen had already replied in his ‘Apologie and True Declaration … of the two English Colleges.’ ‘A True Report of the late Apprehension and Imprisonment of John Nicols,’ containing also the ‘Satisfaction’ of three other recusants—Caddey, Richard Baines, and James Bosgrave—was published at Rheims in 1583 by the Catholics.
Nicholls's letters to Dr. Allen, and a public confession, are printed at the end of Nicholas Sanders's ‘De Schismate Anglicano,’ lib.