The ship was on militia duty when the Spanish–American War began and she was recommissioned in 1898, to defend Baltimore, Maryland, although she was decommissioned later in the year before the necessary refit could be completed.

[5] The exposed sides of the hull were protected by five layers of 1-inch (25 mm) wrought iron plates, backed by wood.

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 protected the crew against Confederate snipers based on a suggestion by Commander Tunis A. M. Craven, captain of her sister ship Tecumseh.

[6] The only known modification after the ship's completion was the addition of a hurricane deck between the turret and the funnel sometime after the end of the Civil War.

[7] The contract for construction of Ajax, originally named Manayunk, after a town in Pennsylvania,[8] was signed by Snowden & Mason, on 15 September 1862.

[10] The ship's construction was delayed by multiple changes ordered while she was being built that reflected battle experience with earlier monitors.

This included the rebuilding of the turrets and pilot houses to increase their armor thickness from 8 inches (203 mm) to 10 inches and to replace the bolts that secured their armor plates together with rivets to prevent them from being knocked loose by the shock of impact from shells striking the turret.

[11] The monitor joined her sisters Oneota and Catawba[12] in ordinary[9] opposite Cairo, Illinois,[12] when she was completed on 27 September 1865,[10] although they drew enough water that they had to be anchored in the main channel where they were often struck by debris, drifting ice, and were vulnerable to accidents.

The ship was assigned to the North Atlantic Squadron and was based at Key West, until she was decommissioned again on 27 July 1875, and laid up at Port Royal, South Carolina.