With the exception of two brief trips to Newport, "Willis A. Lee" remained at the Boston Naval Shipyard until 29 April 1964, when she returned to her home port to prepare for a southern cruise. Underway on 6 May for type training in Guantanamo Bay, the frigate conducted further sonar evaluations later that month en route back to Newport before returning to her home port on 26 May. "Willis A. Lee" subsequently conducted three more evaluation cruises before she participated in Exercise "Steel Pike," the largest peacetime amphibious exercise in history. During those maneuvers, "Willis A. Lee" served as the flagship for Rear Admiral Mason Freeman, Commander, Cruiser-Destroyer Flotilla 2. To then round out the year, the frigate conducted another sonar evaluation cruise, calling twice at Key West during the voyage. She returned north on 11 December and spent the remainder of the year under restricted availability at the Bethlehem Steel Shipyard, East Boston, Mass.