In 1893 The Association for the Preservation of Virginia Antiquities acquired 22 1/2 acres surrounding the old church tower. At that time Mary Jeffrey Gault, founding member of the APVA, began the first excavations to uncover the foundations of the church.

It was long thought that the remains of James Fort were claimed by erosion along the bank of the James River, but some scholars believed the fort was still intact in the vicinity of the 1639 church site. As early as 1902 Samuel Yonge, the engineer responsible for building the seawall, placed the fort between the Confederate earthworks and the church tower.

The National Park Service purchased the rest of the island in 1934 and established the Colonial National Park. With the acquisition of the land came archaeological projects ranging from the W.P.A. projects of the 1930s to the excavations leading up to the 350th anniversary in 1957, most notably by J.C. Harrington in the 1930s and 1940s and John L.Cotter in the 1950s. While Harrington and Cotter are most often associated with previous excavations at Jamestown, a list of the archaeologists who worked at Jamestown reads like a who's who of American archaeology: Edward B. Jelks, Henry C. Foreman, Louis Caywood, Joel Shiner, Frederick Parris, John T. Zaharof, H. Summerfield Day, Conrad Bentzen, and Rex Wilson have all had a hand in the past excavations for the National Park Service.