In 1547 his father and elder brother were convicted of treason and Thomas consequently lost his status as a peer. He was given a general pardon and restored to the rank of baron by Edward VI.[4] His father remained a prisoner in the Tower of London, where Thomas was allowed to visit him in April 1551.[5]
In Elizabeth's reign he apparently adopted a position of outward conformity, but remained under suspicion concerning his religious views. In 1562 he accompanied Bishop Jewel on the ecclesiastical Visitation of the Western diocese, [10] but was omitted by the Privy Council from the commission set up to search for Jesuits and seminary priests in Dorset. However, he was trusted to search the house linked to the Jesuit James Bosgrave in Bere Regis.[11] In 1573 he had prevented John Stourton, 9th Baron Stourton from going abroad for religious reasons.[12] Despite the execution of his nephew Thomas Howard, 4th Duke of Norfolk for treason, Thomas's loyalty to Elizabeth I was never called into question and until the end of his life he was charged with the defence of Dorset's coast.[13]
During the last five years of his life he was engaged in a bitter feud with his son and heir Henry.[15] He died in 1582 and was buried at Marnhull.[16]
Anne Howard (d. 1633) married firstly Sir William Thornhurst(d. 1606) [19], their son Gifford Thornhurst married Susanna Temple, and secondly in 1608 John Turberville of Woolbridge.[20]