Artifacts dating back to the ancient Chamorros have been found along the shore fronting Jeff's Pirates Cove and the surrounding area. They are clues to the rich history of this site, and this internationally known landmark.

Halfway between the Togcha River and the Cove sits a bunker built during World War II when Japanese armed forces occupied the island of Guam. In 1945 Japanese stragglers killed a Chamorro guide and five U.S. sailors who were hunting for war souvenirs up the Togcha River.

Famous W.W.II straggler Sgt. Shoichi Yokoi visited the Cove many times after he was discovered in 1972. For many years a tour to Yokoi's famous cave in Babulao Hills started with a briefing at Jeff's Pirates Cove. He spent 28 years in the Talofofo jungles after the end of the war. Yokoi said that while hiding in the Togcha Hills he listened to the Cove festivities.

Following the war, a Flight Personnel Rehabilitation Camp was built on the site. By 1945 the 25th Naval Construction Battalion built a beer garden, softball diamonds, volleyball courts, and horseshoe pitching pits. Later, a salt water swimming pool was built. After providing for nearly 10,000 officers and soldiers, the camp was devastated in 1949 by Typhoon Allen.

The Cove's original owner found evidence of Malay Pirates having stayed in the area which inspired the name. In 1962 Typhoon Karen hit and wiped out all traces of the Malay village, including a pirate ship scuba divers discovered in 1953.