By the Civil War, Samuel Miller was still alive, though very elderly. Union soldiers pillaged the house, though most of his wealth was hidden away before hand. Though the war had cost him an incalculable amount of money, he managed to gain it back just as quickly by war's end. He would pass away in 1869 at the age of 78.
Currently, the Samuel Miller House is still maintained as a private residence. Other than some alterations made to accommodate modern technology, the house has stayed relatively the same. It was added to the National Register of Historic Places in 1992.