The settlement had a long continuous occupation running from the Middle Formative Period through the Postclassic.
The Late Formative saw the construction of a number of triadic architectural groups linked with roads running north to south.
600–800), the city-state of Coba conquered Yaxuna and built a 100 km Sacbe, or raised road, to connect the two cities.
In the Terminal Classic (800–1100), the state of Chichén Itzá to the north began a war with the Coba state, and Yaxuna constructed a city wall, but Chichén Itzá appears to have conquered the city by around 950.
By the Postclassic (1100–1697), the population was much reduced, with new construction limited to minor additions to older architecture.