A "rifle screen" of 1⁄2-inch (13 mm) armor 3 feet (0.9 m) high was installed on the top of the turret to protect the crew against Confederate snipers based on a suggestion by Commander Tunis A. M. Craven, captain of her sister ship Tecumseh.

[6] The ships needed a deep-water berth and were moved opposite Cairo, Illinois in mid-1865 even though they still had to be anchored in the main channel where they were often struck by debris, drifting ice, and vulnerable to accidents.

Tippecanoe's anchor chain was broken on 27 March 1866 when she was struck by a steamboat towing barges and the monitor collided with Oneota and the two ships were dragged 2 miles (3.2 km) downstream before they could be brought under control.

In August 1867, the Navy turned over Oneota and Catawba to Swift & Co. contingent on a guarantee that they would be returned in good shape if they could not be sold, and the company began refitting them for Peruvian service.

[6] To prepare the ship for her lengthy voyage to Peru around Cape Horn, Swift & Co. added a breakwater on the bow, stepped two masts with a fore-and-aft rig to supplement her engine, and provided closures to make vents and deck openings water tight.

[12] While this was going on, the United States was negotiating with Great Britain over compensation for losses inflicted by British ships knowingly sold to the Confederacy during the Civil War (the Alabama Claims).

They allowed the ship to restock her supplies, but no coal was available so the crew loaded up enough wood to reach the Bahamas where they were able to send a local schooner to Nassau to inform the authorities of their plight.

While entering Rio de Janeiro on the night of 15 September, Manco Cápac ran aground; she was refloated the following day, but the damage required three months to repair.

With the start of this war, the monitor was towed from Callao to the south of Peru to defend the bay of the Peruvian port of Arica, its boilers were repaired and it was propelled at a speed of 2 knots.

The ex-Peruvian ironclad Huáscar failed in her attempt to ram the Peruvian monitor and the Huascar's captain was killed in this engagement of the Naval Battle of Arica.

Manco Cápac hit the schooner Covadonga on blockade duty on 6 June, but the monitor was scuttled to prevent her capture when the city fell the following day.