海军舰队
Despite the losses borne by the Southern Steamship Company, Morgan continued to operate other ventures by doing business with both the Union and the Confederacy. Morgan placed orders with Harlan and Hollingsworth for five large steamers between 1862 and 1864. These ships were frequently booked on charters for the Union during the war. Morgan also profited from his ownership of the Morgan Iron Works, which was producing engines from its shops in New York City for commercial enterprises in the United States and abroad. Beyond civilian production, the Morgan Iron Works built engines and other marine equipment for thirteen ships in the Union Naval fleet. In one case, they built a warship from scratch: . These naval contracts accrued over $2 million in revenue to the Morgan Iron Works. For the Confederates, Morgan ran the "Frances" to evade Union blockades between Havana and the southern ports.