In 1549 a distinguished office was conferred on him, one that his father had held before him, and of peculiar honour in his native county, that of Receiver General of the Duchy of Cornwall. This year, however, the first cloud appeared over his hitherto fortunate career. Himself, with his brother Sir John Arundell of Lanherne, were both suspected of being implicated in the rebellion of their uncle Humphrey Arundell, Governor of St. Michael's Mount, "a man well-esteemed for military services." This was the religious insurrection, demanding the old ritual, and antagonistic to the reformed service of the Church, which began in Cornwall, and gathering strength as it advanced, laid ineffectual siege to Exeter, where, however, the citizens, during their captivity, were reduced to great straits. The insurgents then marched to meet Lord Russell, who was stationed with some force at Honiton, but he defeated them with considerable loss at Feniton (or Fenny) Bridges. They then retreated to Clyst-Heath, near Exeter, where-- "they had brought with them a crucifix upon a cart, covered with a canopy, and beset with crosses, tapers, banners, holy bread and water, as a representation of those things for which they fought." At Clyst-Heath, Lord Gray with his troops, reinforced with those under Lord Russell, dispersed the ignorant priest-led rustics with great slaughter;-- "The dispersion of the insurgents was followed by the same conduct on the part of the royal army, as if they had put to route a foreign enemy in his own country, 'for the whole country was then put to the spoil, and every soldier sought for his best profit.'" Sir Anthony Kingston, as Provost-Marshal of the king's army, was commissioned to try and punish the delinquents, and his cruel and brutal conduct was quite on an equality with that of the wretched Jeffreys on a similar errand a century afterward;-- "Gibbets were set up in various places, on which great numbers of the leaders of the rebellion were hanged. Others, and especially Arundell, the chief captain, were carried to London, and there executed. It was reckoned that about four thousand in all perished by the sword or by the hands of the executioner, of those engaged in this Devonshire (and Cornwall) insurrection." Humphrey Arundell, their uncle, was conveyed to London and hanged at Tyburn in January, 1549-50. And then it is recorded in the Council book,-- "XXX. Jan., 1549-50. Sir Thomas Arundel, Knight, committed to the Tower by order of the board." And further in King Edward's journal,-- "1549. Sir Thomas Arundel and Sir John (his elder brother) committed to the Tower for conspiracies in the west partes."