On 15 September 1541 he was collated rector of St. Nicholas Olave, and on 19 May 1544 rector of St. Botolph's, Bishopsgate. On 17 October 1547 he was appointed archdeacon of Cornwall, and in the same year he became rector of Burton-Overy. Early in 1549 his Catholic views brought him into collision with the university visitors; he was ejected from his professorship, and on 11 September following Alexander Seymour was paid for arresting Weston in Leicestershire and conveying him to the Fleet prison.
In 1556, when it was decided to restore Westminster Abbey to its monastic character, Weston was induced to resign his deanery in favour of John de Feckenham, receiving instead the deanery of Windsor. In Aug. 1557 he was deprived by Cardinal Pole of his deanery and the archdeaconry of Colchester for gross immorality, but retained, through Edmund Bonner's complaisance, his parochial preferments; his moral delinquencies (he was caught committing adultery) are detailed by various Protestant writers of the time, and especially in "Michael Wood"'s preface to the 1553 edition of Stephen Gardiner's 'De Vera Obedientia'. He determined to appeal against Pole's decision to the Roman curia, but was arrested at Gravesend when setting out, and lodged in the Tower of London. He was released on plea of sickness on 3 December 1558, and died at the house of one Winter in Fleet Street on 8 December, being buried in the Savoy. By his will, dated 26 November 1558, he provided for masses for his soul at Balliol and Lincoln Colleges, at St. Mary's, Oxford, at Burton-Overy, and at Islip, of which he is said to have been rector. His Oratio coram Patribus et Clero habita 16 October 1553 was published in that year (London), and disputations are printed in John Foxe's Actes and Monuments. Edward Weston was his great-nephew.