Following the Great Fire of London in 1666, Henry Howard allowed the Royal Society to meet regularly at Arundel House.

[1] He further agreed to bestow his grandfather's collection of manuscripts to the Royal Society, but it initially remained at Arundel House for want of a dedicated library elsewhere.

He later gave away the greater part of his library, grounds, and rooms to the Royal Society, and the Arundelian marbles to Oxford University.

He was presented as a recusant at Thetford assizes in 1680, and felt obliged to return to England to answer the charge, which was not pursued; a previous accusation by the notorious informer William Bedloe in 1678 that he had been party to, or at least aware of a plot to kill the King, had simply been ignored.

He remained in England long enough to sit as a peer at the trial for treason of his uncle, William Howard, 1st Viscount Stafford, a fellow victim of the Popish Plot.

John Evelyn in his diary for 9 May 1683 records visiting him to discuss buying some of his artworks, and gives the diarist's very low opinion of the Duchess.