Mayapan is now receiving new recognition as one of the most important ancient Maya cities. Mexico's Instituto Nacional de Antropología e Historia (INAH) has been restoring the site's monumental center since 1996, and it is open to tourism. These downtown temples, shrines, and colonnaded meeting halls were built and used by important lords and priests of the city's confederated government – restoration has transformed this sector from a jumbled set of rubble mounds overgrown with trees to a majestic appearance of gleaming masonry temples, colonnaded halls, shrines, and altars. INAH's Carlos Peraza Lope has directed this work and he and his team, led by archaeologists Pedro Delgado Kú and Bárbara Escamilla Ojeda have discovered important works of art, including (for example) a mural at the Fisherman Temple and Hall Q-161, life-sized plaster portraits of a set of Mayapan gods at Hall Q-163, large stucco scenes of skeletal deities on the façade of an early phase of the city's principle temple Q-162 (the Temple of Kukulkan), and many fine ceramic effigy incense burner sculptures, including one known as the "monkey scribe." Art historian Susan Milbrath and archaeologist Miguel Delgado Kú have worked with Carlos Peraza to publish analyses of these new artistic programs.

Carlos Peraza Lope, an archaeologist affiliated with the Yucatán office of the National Institute of Anthropology and History, has been excavating and consolidating the major buildings in the ceremonial since 1996. He has uncovered remarkable murals on several buildings. He also found a rather shocking scatter of human bones that may date to the destruction of the site.
Marilyn Masson, of the State University of New York at Albany, directed a major excavation project at Mayapán in the early 2000s in collaboration with Carlos Peraza Lope. She studied the economic structure of the site and found evidence that the site was a major trade nexus.