Sailing from New London, Connecticut, on 21 March 1945, Carbonero served with the Fleet Sonar School at Key West, Florida, and conducted torpedo exercises at Balboa, Canal Zone, before arriving at Pearl Harbor on 9 May.

Her first war patrol, conducted off Formosa from 26 May to 8 July, was devoted to lifeguard duty, standing by for possible rescue of aviators downed in aircraft carrier strikes.

After refitting at Subic Bay, Carbonero cleared for the Gulf of Siam on 4 August, and cruising off the east coast of the Malay Peninsula, sank four schooners, two sampans, and two junks, some of the small remnants of the Japanese merchant fleet.

After a simulated war patrol to the Far East early in 1947, she was assigned to the Submarine Guided Missile Program, joining her sister ship Cusk as a control vessel operating out of San Diego, and Naval Base Ventura County in Port Hueneme, California.

She was on hand for the detonation of a warhead from a Polaris missile fired from Ethan Allen in the "Frigate Bird" nuclear weapon test.

During the mid 1960s while operating off Kaena Point, Oahu, Carbonero ran aground at a depth of 250 feet (76 m), requiring drydock repair at Pearl Harbor Naval Shipyard.