Downfall and death
By the late 1530s, Courtenay was an influential figure at court and was administering most of western England in his own name and in that of King Henry VIII. He was also a political rival of Thomas Cromwell and the two men reportedly had little sympathy for each other.
Following the Reformation, Courtenay's second wife, Gertrude Blount, remained a Roman Catholic. She had supported Elizabeth Barton to her downfall and continued to maintain correspondence with the Catholic former queen Catherine to her death. Her father had served as Queen Catherine's chamberlain, and a stepmother had been one of her Spanish attendants while she was Princess of Wales. Cromwell used these connections to point suspicion at Courtenay's loyalties.
Being a powerful landowner in the west country did not make him blind to the sufferings of his tenants. Many lay and clerical alike were turned out of their lands and homes by the Dissolution of the Monasteries and Courtenay came to hate Vicar-General Cromwell and his Protestantism, whose "measures ... became so obnoxious to him that he drifted into a treasonable conspiracy with the Pole family". He joined the Catholic Poles in the Western Rebellion during 1538 and endeavoured to raise the men of Devon and Cornwall. At St Keverne on the Lizard peninsula of Cornwall a painted banner was reportedly created which was taken around local villages and called for the population to revolt.
However, Madeleine Hope Dodds argues that there never was a conspiracy. "They were less a political party than a group of friends, who loved the old Faith, hated Cromwell, and longed for a change of policy. They met and talked treason and sang political songs... They did not trouble themselves about anything so strenuous and intellectual as a plot." Bernard Burke says Exeter fell victim to the king's jealousy of the Poles.
Courtenay was found to be in correspondence with the self-exiled Cardinal Reginald Pole. Geoffrey Pole, younger brother of the Cardinal, came to London with the information that a Roman Catholic conspiracy was in the making. Both Poles were accused of heading this conspiracy and Cromwell convinced the king that Courtenay was a part of it. Perhaps anticipating the end, he wrote a will on 25 September 1538.
In early November 1538, Courtenay with his wife and son Edward Courtenay were arrested and incarcerated in the Tower of London. On 3 December 1538 Courtenay was put on trial by his peers in Westminster Hall, although there was little evidence for his involvement in the so-called Exeter Conspiracy. He was found guilty because of his correspondence with Cardinal Pole in Rome. Courtenay was beheaded with a sword on Tower Hill on 9 December 1538, with Henry Pole, 1st Baron Montagu, who was the elder brother of both the Cardinal and Geoffrey, together with their cousin Edward Neville. He was attainted and the Earldom of Devon became forfeit, and his lands in Cornwall were annexed by the Duchy of Cornwall.
His wife Gertrude and his son Edward were both attainted in 1539, when her lands (including estates inherited from Sir William Say) were forfeited to the Crown. She was released in 1540 and maintained a friendship with the king's elder daughter, Mary, for the rest of her life. Following Mary's accession, on her orders his son Edward Courtenay was released on 3 August 1553, and thereafter became a suitor for her marriage.