Returning to his post as a member of Parliament, he would command a division consisting of around 5,000 soldiers during the First Miguelist War where he attempted to support Portuguese forces from December 1826 until April 1828. Promoted a full general, Clinton resigned from Parliament serving as governor of Chelsea Hospital from 1842 until his death on 15 February 1846 on Cockenhatch, near Royston, Herts. There is a memorial plaque to Clinton in St. Mary Magdalene Church, Barkway, Herts.