After the death of Mary, Elizabeth succeeded to the throne. The Council ordered him to resign the bishopric, which he refused to do, adding that he preferred death. He was sent again to the Marshalsea prison on 20 April 1560. During the next two years representatives of the Protestant party frequently clamored for the execution of Bonner and the other imprisoned bishops. When the Parliament of 1563 met, a new Act was passed by which the first refusal of the oath of royal supremacy was "praemunire", the second, high treason. The bishops had refused the oath once, so that by this Act, which became law on 10 April 1563, their next refusal of the oath might be followed by their death. Thanks to the intervention of the Spanish ambassador, action against the bishops was delayed; but a year later, on 29 April 1564, Bonner was indicted on a charge of "praemunire" on refusing the oath when tendered him by his diocesan, Bishop Horne of Winchester. He challenged the legality of Horne's consecration, and a special act of parliament was passed to meet the point, while the charge against Bonner was withdrawn. Four times a year for three years he was forced to appear in the courts at Westminster only to be further remanded. The last of these appearances took place in the Michaelmas term of 1568, so the last year of the bishop's life was spent in prison. His demeanor during his long imprisonment was remarkable for his cheerfulness, and even John Jewel, the Bishop of Salisbury, describes him in a letter as "a most courteous man and gentlemanly both in his manners and appearance" ("Zurich Letters", I, 34).