In 1564 he distinguished himself by his ability in the theological disputations before Queen Elizabeth at Cambridge, and his character was established as one of the ablest scholars and preachers in the university.After his appointment in April 1567 as dean of York he resigned his mastership at Pembroke, the regius professorship, and his canonries of Ely and Westminster.A letter to Burghley, dated 6 October 1573, is preserved at Hatfield, giving at length his opinions on prevailing differences in church government.He was suspected of leaning to the Puritans, and this led to a dispute with Archbishop Sandys, who in 1586 preferred a charge of thirteen articles against him.He acted as lord president of the north from 1595 to 1600, and in 1598 he had in his custody at Bishopsthorpe Sir Robert Ker of Cessford, one of the wardens of the Scottish Marches.One of his last public acts was to write a letter to Robert Cecil, Lord Cranborne, counselling a relaxation in the prosecution of the puritans.
Modern stained glass window in Warton Church showing Hutton holding an architectural drawn plan of the church, with his arms as Archbishop of York
Monument with semi-recumbent effigy of Archbishop Matthew Hutton in the south choir aisle of
York Minster
, showing his arms as Archbishop of York and as Bishop of Durham