Shortly thereafter he made original contributions to the field of decipherment and began working closely with the noted Mayanist Linda Schele, focusing on the art of inscriptions of Palenque.

However, only a limited amount of Maya texts could be read in their original language, Classic Mayan, due to an imprecise understanding of the visual nature of the script, especially the ways signs formed and combined.

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.

In 2018 he presented a new interpretation of the so-called Calendar Stone of Tenochtitlan, suggesting it is not an image of an Aztec deity, but rather a deified portrait of the emperor Moctezuma II as the sun.

In 2003 he published a volume in the ongoing Corpus of Maya Hieroglyphic Inscriptions series (Peabody Museum, Harvard University), devoted to drawings and photographs of sculpture from Piedras Negras, Guatemala.

[2] He also oversees the activities of the Casa Herrera, UT's academic research center in Antigua, Guatemala, devoted to studies in the art, archaeology and culture of wider Mesoamerica.