For the remainder of her career, "Willis A. Lee" continued in her routine of sonar development and testing, home-ported out of Newport with occasional periods of yard repairs at Boston. During her final years, the frigate operated off the Virginia capes, in the Caribbean, and Narragansett Bay areas, and was deployed to the Mediterranean November 1966. She returned to Newport on 20 May 1967, thus completing her first extended deployment since 1961. She was deployed again to the Mediterranean January 1968, returning to Newport in May of that year. In August 1968, she was deployed to the Red Sea as the flagship for COMMIDEASTFOR. However, what was to be a 10-month deployment was cut short when she developed propulsion problems while in transit off the coast of Brazil. After undergoing two weeks of repair in Recife, Brazil, she was relieved by USS Luce (DLG-7), and returned to Newport. In January 1969, she transited from Newport to the Boston Naval Shipyard via the Cape Cod Canal for what was to be her final overhaul prior to decommissioning later that year.