[3] Isabel II was assigned to duty at Fernando Po in the Bight of Biafra off the coast of West Africa, where she replaced the screw schooner Ligera.

[3] The protected cruiser Marqués de la Ensenada replaced her early in 1893, and Isabel II began her return to Spain, setting course for Cádiz.

Isabel II was at San Juan, Puerto Rico, with the destroyer Terror, the gunboats General Concha and Ponce de León, and several smaller vessels when the war broke out.

Terror attempted to cover Isabel II′s withdrawal by making a torpedo attack, but Saint Paul thwarted it by putting Terror′s rudder out of action.

[5] On 16 June 1898, a Spanish blockade runner carrying a cargo of food, ammunition, and 12 artillery pieces for Spanish forces on Puerto Rico, the merchant steamer Antonio Lopez got underway from Cádiz with the Philippines-bound squadron of Contralmirante (Counter Admiral) Manuel de la Cámara, then parted company with Cámara to proceed independently to San Juan.

[12][13] The Spaniards managed to salvage almost all of Antonio Lopez's cargo, losing only one artillery piece overboard,[14][15] before New Orleans returned on 16 July to sink her wreck with gunfire.

On September 14, 1898, Isabel II left Puerto Rico bound for Spain with Terror, General Concha, and Ponce de León.

Deemed lacking in combat value and not worth the cost of further maintenance or repair, she was decommissioned on 18 May 1900 and hulked as a floating jetty and torpedo boat school at Cartagena.