He was imprisoned on suspicion of Jacobitism from May to July 1689 and again in June 1690, but no charges were ever successfully brought against him. After his release, he retired from public life at age 57. He moved out of London ten years later (1701) to a house in Clapham owned by his friend William Hewer, who had begun his career working for Pepys in the admiralty. Clapham was in the country at the time; it is now part of inner London.