She was relieved as flagship by Lancaster on 17 June 1869 and sailed from Rio de Janeiro the 25th for the New York Navy Yard where she decommissioned on 29 July 1869.

At Portsmouth, New Hampshire, 27 September, she received the body of the late Admiral David Farragut for transport to New York.

The following day she went fast aground on Great Point, Nantucket and transferred Admiral Farragut's remains to merchant steamer SS Island Home.

On 7 April 1871 she was host to the pasha of Tripoli, who inspected the ship and presented Guerriere's captain with the anchor of the frigate Philadelphia.

This anchor had laid on the beach for more than half a century after the destruction of the frigate in Tripoli Harbor by Captain Stephen Decatur in "the most bold and daring act of the age".