"Juniata" received orders on 23 February to cruise along the coast of Brazil as far south as Buenos Aires protecting American citizens and interests. 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. With the exception of a cruise to the coast of Africa from 12 June to 30 September 1866, she remained in South American waters until 30 April 1867 when she sailed from Rio de Janeiro for home, arriving Philadelphia on 24 June.