 Somerset was arrested at Windsor on 11 October 1549, and on 13 October Thynne was sent to the Tower with William Grey, Sir Thomas Smith, Sir Michael Stanhope and Edward Wolf, these being described as the Duke's "principal instruments and counsellors... in the affairs of his ill government".In August 1550, he was pardoned and all his goods and offices were restored, but he was put into the Tower again on 16 October 1551.After Somerset's execution, like his other followers who were spared, Thynne lost his offices and much of his land, and he was heavily fined.