In 1504, during the reign of the Tudor King Henry VII, William Courtenay was accused of maintaining correspondence with Edmund de la Pole, 3rd Duke of Suffolk, the leading Yorkist claimant to the throne, and the king ordered him incarcerated in the Tower of London and he was attainted in February 1504, which disabled him from inheriting his father's earldom.

William enjoyed some favour with Henry VIII who reversed his attainder on 9 May 1511 and created him Earl of Devon on 10 May 1511, with the usual remainder to heirs male of his body.

[citation needed] In April 1522 he was made keeper of Burling Park in Kent, during which period he reached his greatest height of power in the king's inner council.

Henry VIII sent the new Marquess of Exeter to secure an agreement with French regent Louise of Savoy and to pledge the assistance of the English king in negotiations for the return of Francis.

The Marquess of Exeter further served the interests of the King in the proceedings for the annulment of his marriage to Catherine of Aragon and signed the letter to Pope Clement VII in that regard.

He was placed second to the King at the Privy Council at which Cardinal Thomas Wolsey was charged with treason and signed the documents for his prosecution.

In 1536 Courtenay was a commissioner at the trial of Anne Boleyn, the king's second wife who had been accused of adultery, incest, and high treason.

Courtenay and Charles Brandon, 1st Duke of Suffolk were sent into Yorkshire to put down the Pilgrimage of Grace, a Roman Catholic uprising that broke out on 15 October 1536.

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".

[2] 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.

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.

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.