Post-Civil War
After the Civil War, Luce organized the Navy's apprentice training program to prepare naval seamen and petty officers for fleet duty. From 1869 to 1872, he commanded the sloop-of-war USS Juniata which was assigned to the Mediterranean Sea Fleet. He was promoted to captain in December 1872 and served as the captain of the yard at the Boston Navy Yard (at Charlestown, Massachusetts, across the Charles River from Boston), until 1875. He commanded the USS Hartford from November 1875 to August 1877. From August to December 1877, Luce was the Navy's inspector of training ships, then from January 1878 to February 1881, he commanded the training ship USS Minnesota.
From July to September 1884, Luce commanded the North Atlantic Squadron with the USS Tennessee as his flagship. From June 1886 to February 1889, Luce again commanded the North Atlantic Squadron with the USS Richmond this time as his flagship.
Luce helped start the United States Naval Institute in October 1873; he would serve as the Institute's president from 1887 to 1898.
In 1881, Luce was promoted to commodore, and commanded the U.S. Navy Training Squadron in Newport from April 1881 to June 1884.
While in command of the Training Squadron, Luce developed and implemented the apprentice training program—the first formal program for training American enlisted sailors. Luce's plan was to have bright and healthy young men, 14 to 17 years old, serve an apprenticeship with the Training Squadron during which they received an academic education and hands-on seamanship training.
The "boys" were typically enlisted around 14 or 15 and typically served in the Navy until age 21, when they could choose to be discharged or extend their service in the Navy. Previously, the Navy had taken recruits with no prior experience; all training of enlisted sailors was "on the job". Many recruits lacked the discipline and skills necessary to be useful. The program ended in 1904 when the Navy was rapidly expanding and could not wait several months for new recruits to be trained.
Based on Luce's urgings and exhaustive reports, the Naval War College at Newport, Rhode Island, was established on October 6, 1884. Luce served as its first president. In 1885, he was promoted to rear admiral, and the next year handed off the presidency to Captain Alfred Thayer Mahan.