After Theodore Roosevelt (with whom he was friends at Harvard) had been reelected, Bacon was named Assistant Secretary of State in 1905, a position which he held until 1909; he was acting secretary while Elihu Root was in South America in 1906. For the last 38 days of Roosevelt's term, he became full secretary from January 27 to March 5, 1909, because of Root's election to the Senate. Bacon obtained the advice and consent of the Senate for the Panama Canal treaties with Colombia and Panama. He served as United States Ambassador to France from 1909 until 1912. He was supposed to return home on the RMS "Titanic" with his wife and daughter, but delays kept them in Paris.