[1] He enlisted in the US Navy as a midshipman in April 1804 and saw action in the Mediterranean Sea during the Barbary Wars between 1805 and 1807, serving on board the USS Essex under Commodore James Barron.

He was promoted to master commandant in July and reassigned to the Lake Erie squadron, to serve as Commodore Perry's second-in-command.

During the Battle of Lake Erie against a British squadron under Captain Robert Barclay on 10 September, Elliott commanded the brig USS Niagara.

After the Lawrence was battered into a wreck, Perry took command of the Niagara while Elliott was dispatched by boat to urge the smaller American gunboats at the rear of the line of battle into closer action.

Elliott won distinction for his actions and official praise from Perry, and was given command of the Lake Erie squadron the next month.

In addition to the medals, Elliott and Perry each received an equal share of the prize money ($7,140.00 apiece) for the capture of the British squadron at Lake Erie.

Decatur's widow published the charges made by Perry years later as she held Elliott to be at least partially responsible for her husband's death.

Elliott commanded the sloop USS Ontario during the Second Barbary War, and was promoted to Captain in 1818, serving on a naval commission selecting sites for navy yards, lighthouses, and other coastal fortifications, until 1822.

Elliott was appointed commander of the Boston Navy Yard in 1833 and of the frigate USS Constitution and the Mediterranean Squadron from 3 March 1835 to 18 August 1838.

During the Mediterranean assignment, he was charged with minor offenses by several of his junior officers, including using his official position for personal gain and transporting animals he had purchased aboard Constitution.