Arundell was connected by birth and marriage to the crown and to several of the most important families in England, and by the time of the death of King Henry VIII was one of the most experienced government officers in England. However, those in power at the beginning of the reign of King Edward VI removed his name from the late King's list of proposed honours, reflecting their concern with his influence and his family's devotion to the old religion. Vague and unproven allegations of complicity in the south-western rebellion in 1549 were made against him and against his brother, Sir John Arundell (c.1550–1557), leading to their imprisonment in 1550 and again in 1551, and marking the end of Sir Thomas Arundell's career. In late 1551 he temporarily aligned himself with the Protector Somerset, thereby putting himself in conflict with John Dudley, Earl of Warwick. He was arrested and charged with conspiring to overthrow the government and murder the Earl. Arundell consistently protested his innocence, but was convicted, beheaded on Tower Hill on 26 February 1552, and buried in the Church of St Peter ad Vincula. His property was confiscated, although in June 1552 the Crown began restoring it to his widow and, from 1553, to his son Matthew Arundell. His widow, Margaret, died 10 October 1571, and was buried at Tisbury, Wiltshire.