The San Diego History Center initiated the Presidio Excavation Project in 1965 to discover and identify what lay below the grounds. Since the museum was not built upon the old presidio ruins, it was expected that the foundation walls would be uncovered. The project was undertaken as a cooperative effort between the Historical Society and local colleges with approval of the City of San Diego.
Research into archives in Spain, Mexico and California failed to unearth any maps or drawings of the original presidio, so digging began in the area thought to be the soldiers' barracks. The chapel complex was excavated by students from San Diego State University, Mesa College, and selected volunteers under the direction of Dr. Paul H. Ezell. Members of the locally prominent Bandini and Estudillo families had been married in the chapel and it was used as late as 1841 by the people living in the pueblo - today's Old Town.
In addition to chapel foundations, students unearthed animal bones, sea shells, potsherds and other material revealing the dietary habits of the first settlers. Detailed drawings of the chapel were made and the foundations covered over for protection. Excavations were also made into burial sites in the presidio cemetery located at the side of the church. An important discovery made in February, 1968, was the grave of pueblo settler Henry Delano Fitch who died in 1849. Other graves were also found.
Mesa College, in 1976, began to search for the main entrance into the presidio on the northwestern side of Presidio Drive. Many additional artifacts have been uncovered which are on display in the Serra Museum with explanatory information. The San Diego History Center, under an agreement with the City, provides interpretative services of the areas under investigation and escorts groups of twenty or more touring the presidio area. The park itself is an outdoor museum that is continually evolving. Each new discovery contributes another piece to the puzzle and helps tell the story of Serra's San Diego.