Phelps died at his New York residence, formerly the Coster place, on 30 November 1853 at age 73. He left about two million dollar, of which almost seven hundred thousand was his shares in Phelps Dodge & Co. These were purchased by the other partners. Just over one million dollars was property in New York, Indiana, Connecticut, Pennsylvania and Missouri. His will was contested and there were so many anomalies that his widow, who was the executrix, put it before the courts to sort out. It was after her death that the final verdict was given by the court of appeal in 1861. Due to a technical issue with the wording of the will, one large bequest of $50,000 to the Liberia College was declared void by the courts. However, the family held this bequest to be sacred and the donation stood despite the ruling.