Ticonderoga went south on 5 June 1863 for duty as flagship of the West Indies Squadron and, after stopping at Philadelphia, arrived at Cape Haitien on 12 June. She patrolled waters off the Virgin Islands, Barbados, Tobago, Trinidad, and Curaçao protecting Union commerce. Ticonderoga returned to Philadelphia for repairs in September. She was relieved as flagship of the squadron in October and sent to the Boston Navy Yard. Ticonderoga joined the South Atlantic Blockading Squadron on 19 January. After a brief tour of duty, she left for Philadelphia in March and was decommissioned there on 5 May.