Maní has been continuously occupied for approximately 4,000 years. In the postclassic Mesoamerican era it was home to the Tutal Xiu Maya dynasty, which moved their capital here from Uxmal in the 13th century. The Xiu were the dominant power in the western Yucatan after the fall of Mayapan in 1441. A yearly festival in honor of the deity Kukulcan was held here.
With the arrival of the Spanish the Xiu of Mani allied themselves with the Spanish and assisted in the conquest of the rest of the peninsula.
The town has an old Franciscan monastery established in 1549, the Parroquia y Exconvento de San Miguel Arcangel. The large building was build using many cut stones from Pre-Columbian buildings of Maní. Inside are some early colonial era fresco murals. Restoration work on the monastery building and its artwork began in 2001.