He worked in the business world, including partnership with J.P. Morgan & Co. for many years starting in 1894. He acted as J.P. Morgan's chief lieutenant and participated in the formation of the U.S. Steel Corporation and the Northern Securities Company. The pressure of the job shot his nerves, and he left the company in 1903.
He was named Assistant Secretary of State in 1905, a position which held until 1909— he was acting Secretary while Elihu Root was in South America in 1906. Bacon obtained the advice and consent of the Senate for the Panama Canal treaties with Colombia and Panama. He became a Fellow of Harvard in 1912. In August 1914 he went to France to help with the work of the American Ambulance. His book For Better Relations with Our Latin American Neighbors was published in 1915. He was then commissioned a major and detailed to General Pershing's staff in 1917, promoted to lieutenant colonel in 1918 and served as Chief of the American Military Mission at British General Headquarters.