Returning to the war in 1864, Hamilton was promoted to Lieutenant Colonel and served in Powers' Brigade, commanding a cavalry battalion. Following the war, he moved to Jackson, Mississippi, which became his permanent residence. He then served as a member of the Mississippi Peace Commission that traveled to Washington in 1865 to meet with President Andrew Johnson. Over the next few years, Hamilton continued to hold public office, serving as a war claims agent for the state of Mississippi throughout 1866, and later becoming deputy auditor. He was also a leading partner in a printing firm, Hamilton and Power Company, that was responsible for producing the Daily Clarion Ledger between 1865 and 1867.
Records indicate the youngest son died in childhood.
Hamilton later donated the house, and it became Belhaven College. Unfortunately, the building was destroyed by fire in 1895. Already a well-known figure in the Jackson area, Hamilton achieved statewide notoriety in 1887 following his arrest for the murder of Roderick Dhu Gambrell, a young newspaper editor. Apparently, the two men held opposing views on the issue of using prison inmates for private labor. Gambrell had written several editorials criticizing the views of Hamilton and had stood against Hamilton in a local election.