Scheduled for service in the West Indies, Juniata was temporarily assigned to the North Atlantic Blockading Squadron and stationed at Norfolk, Virginia, where her guns could help defend the area while machinery defects were corrected at the Navy Yard.

She departed Hampton Roads for the West Indies on 26 April 1863 and four days later captured schooner Harvest bound for Nassau, New Providence, with a cargo of cotton.

She captured English steamer Victor about 8 miles off Morro Castle, Cuba on 28 May, and on 13 June took the schooner Fashion, loaded with chemicals critically needed by the Confederacy.

Juniata continued to cruise in the West Indies convoying California-bound ships to safe waters and alertly watching for signs of Confederate cruisers and blockade runners until she sail for New York on 24 November, arriving there 2 December.

After a brief visit to Port Royal, South Carolina, to repair some of the damage sustained in the furious action at Fort Fisher, she participated in the expedition to Bull's Bay in support of General William Sherman's drive north through 17 February.

After extensive repairs she departed Port Royal on this assignment on 17 June and arrived Bahia, Brazil, 8 August bringing that city its new United States consul.

After a cruise to the Caribbean, Juniata sailed for the European Station on 6 May 1874 and remained on duty there until she returned to the United States, arriving Baltimore, Maryland on 6 February 1876.

George Dewey in command, and departed on a voyage which took her around the world through the Strait of Gibraltar, the Suez Canal, to Bombay, Batavia, Singapore, and Hong Kong, among her many ports of call.