Stuart has also contributed a number of studies of Maya art, history and religion, especially at the sites of Copán, Palenque, Tikal, La Corona, San Bartolo and Xultun. in the late 1990s he produced a new interpretation of the history surrounding the Teotihuacan's "arrival" to the Maya area in 378 CE, proposing this was a military overthrow of the local Tikal king, and the establishment of a new political order. Much of Stuart's work focused on the field documentation of Maya sculpture and inscriptions at numerous sites, through epigraphic drawing and photography. He remains actively engaged as a member of several ongoing excavation projects in Guatemala, Honduras and Mexico.