Beginning in the 1960s, professional archeological investigations sought to determine the exact location of the mission. During the 1970s-1980s, archeologists from Stephen F. Austin State University in Nacogdoches led field schools in the area and confirmed the location where Mission Dolores once stood.
Although construction of Highway 147 destroyed a significant portion of the site and no above-ground features remained, excavations revealed middens, wells, post holes, wall remnants, and other 18th-century features. Many artifacts including lithic, ceramic, metal, and faunal items relating to the Spanish, French, and Ais cultures were recovered. In the early 1990s, the City of San Augustine acquired the site, preserving the archeological remains and creating a museum.
In 2016, the City of San Augustine asked the Texas Historical Commission (THC) to assume ownership of the site, which is listed in the National Register of Historic Places and is also a designated State Antiquities Landmark. The THC welcomed Mission Dolores as an official state historic site that year.