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.
On 18 September 1553 he was installed dean of Westminster, and on 22 January 1554 was collated to the archdeaconry of Colchester; he also received the living of Cliff-at-Hoo, Kent, on 2 April 1554, resigning the rectorship of Lincoln in 1555.
In August 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[2]) 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'.
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.