Although unprotected and therefore lacking armor, she had 12 watertight compartments built in a French-style cellular system to help her resist flooding.

By 1897 she was anchored in Havana harbor in Cuba, serving as flagship for Admiral Vincente Manterola, but she was unable to put to sea because her boilers required a major refit, and some of her guns had been put ashore to aid in the harbor's shore-based defenses.

Amid growing tensions between the United States and Spain, the U.S. battleship Maine arrived in Havana harbor unexpectedly on 25 January 1898.

Her commanding officer, Captain Charles Sigsbee, fearing Spanish mines, requested that Maine be allowed to anchor in the berth occupied by Alfonso XII, where he presumed there could be no mines, but the cruiser's immobility forced him to accept an anchorage about 200 yards (180 m) away.

The crew of Alfonso XII was heavily involved in rescuing the battleship's survivors, treating them in the cruiser's sick bay, and guarding the battleship's wreck, and marched in the funeral cortege during services ashore in Havana for the men who had died aboard Maine.