[2][3] During the next two years, she helped guard the lower Mississippi River, returning to New York Navy Yard where she decommissioned April 29, 1864, for the installation of new and improved machinery originally intended for the cancelled sloop-of-war USS Wanaloset.

While in the harbor of Coquimbo, Chile, on 30 July 1873, Ordinary Seaman Patrick Regan jumped overboard and rescued a drowning shipmate, for which he was later awarded the Medal of Honor.

[4] But for two periods in ordinary, February 15, 1870 to October 14, 1871, and December 31, 1873 to July 13, 1874, Pensacola continued this duty until detached from the Pacific squadron in June 1883.

Departing Callao, Peru on July 18, she sailed west across the Pacific and Indian Oceans, transited the Suez Canal, and steamed the length of the Mediterranean Sea before crossing the Atlantic to arrive in Hampton Roads on May 4, 1884.

Recommissioned April 4, 1885, Pensacola, under the command of then Captain George Dewey, operated in European waters until returning to Norfolk in February 1888 for repairs.