"San Jose" was decommissioned and transferred to Military Sealift Command on 2 November 1993. She was deployed to East Timor as part of the Australian-led INTERFET peacekeeping taskforce from 25 to 31 October 1999. In 2005, "San Jose" provided logistics support to hospital ship in efforts to provide assistance to victims of the December 2004 tsunami in Southeast Asia. "San Jose" most recently provided logistics support to Navy ships in the Persian Gulf supporting both Operation Enduring Freedom in Afghanistan and Operation Iraqi Freedom.