At the Restoration, Digby found himself in favour with the new regime due to his ties with Henrietta Maria, the Queen Mother. However, he was often in trouble with Charles II, and was once even banished from Court. Nonetheless, he was generally highly regarded until his death, a month before his 62nd birthday, from "the stone", likely caused by kidney stones. He was buried in his wife's tomb (which was damaged in the great fire of 1666), in Christ Church, Newgate Street, London.