Willis A. Lee was decommissioned on 19 December 1969, stricken from the Naval Vessel Register on 15 May 1972 and sold for scrap to the Union Minerals and Alloys Corporation of New York City on 18 May 1973.

Upon the conclusion of her first tour with the 6th Fleet later that year, Willis A. Lee returned to the east coast and operated off the eastern seaboard in air defense exercises.

In February 1956, Willis A. Lee — reclassified as a frigate in 1955 — sailed southward to the Dominican Republic, where she represented the United States in American Day festivities at Ciudad Trujillo, the capital city of that West Indian nation.

In November 1956, while participating in anti-submarine warfare (ASW) exercises, Willis A. Lee assisted the distressed fishing vessel, Agda, off Montauk Point, Long Island, fighting and extinguishing a blazing oil fire and thus saving several lives.

That spring, Willis A. Lee played "movie star", when she was filmed by the Louis de Rochemont studios for a part in the cinerama production, "Windjammer", while she operated on ASW exercises in the North Atlantic.

She subsequently participated in the International Naval Review held that summer at Hampton Roads, Virginia, before becoming part of a large combined NATO fleet that conducted intensive ASW and air defense exercises in the North Atlantic that autumn.

In the summer of 1959, she participated in Operation "Inland Sea" as flagship for Rear Admiral E. B. Taylor, Commander, Task Force 47, on a cruise on the Great Lakes.

During that historic voyage, she transited the newly opened St. Lawrence Seaway and visited the ports of Chicago, Illinois; Milwaukee, Wisconsin; Detroit, Michigan; Erie, Pennsylvania; and Cleveland, Ohio.

After a brief trip to Charleston, S.C., in August, Willis A. Lee participated in Operation "Sword Thrust," a NATO fleet exercise in the North Atlantic which combined the efforts of more than 60 British, French, Norwegian, Canadian, and American warships.

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 Guantánamo Bay, the frigate conducted further sonar evaluations later that month en route back to Newport before returning to her home port on 26 May.

She subsequently conducted type training off the Virginia capes and in the Narragansett Bay area before arriving at the Boston Naval Shipyard on 30 June to commence a lengthy overhaul to her engineering plant and modifications to her sonar system.

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.