On 5 January 1905, "Topeka" stood out of Newport News, Virginia, to return to the West Indies. She stopped at Key West for 11 days, from 11 to 22 January and then continued on to Cuba. Between 23 and 25 January, the warship gathered hydrographic and commercial information at Havana. She coaled at Bahia de Nipe on the 27th and headed for Puerto Rico, where she trained with the North Atlantic Fleet until 17 February. She operated out of Guantanamo Bay from 19 February to 22 March and then headed back to the United States. After visits in Florida at Key West and Pensacola, "Topeka" arrived in Hampton Roads on 11 April. On the 23rd, the gunboat again headed south to the troubled waters of the West Indies. She arrived off the Dominican Republic on the 28th and patrolled the coastline of that strife-torn country into August. On 13 August, the gunboat weighed anchor at Guantanamo Bay and shaped a course for Portsmouth, New Hampshire, where she arrived on the 21st. "Topeka" was placed out of commission on 7 September 1905 and assigned duty as station ship at Portsmouth.