After Cromwell's fall he left court and retired into the country, where in May 1542 he was credited with an intention marry and keep a grammar school.
Before the end of Henry VIII's reign Traheron found it advisable again to go abroad, and in 1546 he was with John Calvin at Geneva.
Traheron gradually abandoned Bullinger's views, and adopted Calvin's doctrine of predestination and anti-sacramentarian dogmas.
[1] The main question at the time was the doctrine of the Eucharist to be adopted in the Book of Common Prayer, on which the Windsor commission was then sitting.
On 14 December of that year he was on John Cheke's recommendation appointed keeper of the king's library with a salary of twenty marks in succession to Roger Ascham, and in February 1549–50 the council nominated him tutor to the young Henry Brandon, 2nd Duke of Suffolk at Cambridge.
Traheron was not in holy orders, but on 29 September the council wrote to the chapter of Chichester Cathedral urging his election as dean.
In 1557 he published 'An Exposition of a parte of S. Iohannes Gospel made in sondrie readinges in the English congregation at Wesel by Bartho.
Traheron to a privie papiste which crepte in to the English congregation of Christian exiles ...,' Wesel?, and 'A Warning to England to repente and to turn to god from idolatrie and poperie by the terrible example of Calece given 7 March Anno C. 1558 by Benthalmai Outis [i.e. Bartholomew Traheron], ...,' Wesel?
He published also 'Ad Thomam fratrem Parænesis,' Frankfurt, 1538, has verses in 'Johannis Parkhursti Ludicra sive Epigrammata,' 1573, wrote various letters to Bullinger which are printed in 'Original Letters' (Parker Society), and is credited by John Bale with the authorship of 'In mortem Henrici Dudlæi carmen i.,' ‘In mortem senioris Viati [Wyatt] carmen i.,' ‘In testamentum G. Tracy lib.