According to mythology, the god Huitzilopochtli abandoned his sister Malinalxóchitl because she was practicing evil witchcraft. While she slept, he left her in the middle of the forest. When she woke, she was furious at having been abandoned by her brother. She gathered people loyal to her and marched off to settle in what is now Malinalco.[1] Another version of the story has Malinalxóchitl as the leader of a dissident Mexica tribe, who left to settle in what is now Malinalco and intermarried with the people already there.[2]

Since far in the pre-Hispanic past, Malinalco was considered a magical place, filled with gods and sorcerers.[3][4] The area shows influences from the Teotihuacan culture, the Toltecs, Matlatzincas and Aztecs,[5] but little is known of the area’s pre-Aztec history. Remains of an earlier ceremonial center exist at the summit of the Cerro de los Idolos (Hill of the Idols), but this center and its associated residential zones have not been excavated.[2] The first settlements in this part of Mexico State date back to the early post-Classic and the beginning of the late post-Classic. This was a time when many populations were on the move in the highlands of Mexico, with new peoples moving south from what is now northern Mexico. The first people to arrive here were probably the Culhuas, led by a chief named Cuauhtepexpetlatzin, after this group had already settled in the Valley of Mexico. Other peoples to arrive here include the Matlazincas, the Ocuiltecos and the Otomi.[6] By the time the Aztecs arrived, the area was dominated by the Matlazincas, who had settled earlier in the Toluca Valley by 8th century CE, then migrated here.[2] By the mid-15th century, the Aztecs and the Matlazincas had something of an understanding. However, in 1476, the Aztecs subjected this area to their empire under the rule of Axayacatl.[6] While Axayacatl conquered this area, it was a successor, Ahuizotl who had most of the Aztec shrines, temples and other constructions built here.[7] including the fort and sanctuary for Aztec military elite.[4] When the Spanish arrived, the inhabitants of Malinalco resisted the conquistadors. Andrés de Tapia was in charge of subduing the populations of Malinalco and Ocuilán. Once this was achieved, the area was organized into encomiendas. Malinalco was first under the jurisdiction of Cristobál Rodriguez de Avalos and then the Spanish Crown itself.[6]

The Franciscans were the first to arrive and begin the evangelization process, followed by the Dominicans. However, it was the Augustinians who stayed and built the monastery from which evangelization would center. This monastery was originally called San Cristobál but later the named was changed to Divino Salvador. After the construction of the Temple of the Divino Salvador, neighborhood chapels were constructed in the various parts of town. It is likely that these chapels started out as simple thatched roof structures.[6] During the colonial period, a communal water supply system was developed, taking advantage of the natural water flows in the box canyon that surrounds the town.[8] The Jalmolonga Hacienda was one of the economic focuses of the area, which was part of the Rodriguez encomienda. Later, when the Jesuits came, they took over this hacienda, which was productive enough to support many of the expenses of the San Pedro and San Pablo College located in Mexico City. When the Jesuits were expelled in the 18th century, this land was eventually sold to the Count of Regla, Manuel Romero de Terreros.[6]

During the Mexican War of Independence, José María Morelos y Pavon came through here in 1813, signing a document acknowledging the local indigenous laws regarding agricultural practices, and demanding the withdrawal of an ecclesiastical request to send money to Spain to fight the French.[6] While Benito Juárez and the liberals won the Reform War in 1861 against the conservatives, conservatives in the Malinalco area continued to fight for a while from the mountains. When the Reform Laws were applied against the Monastery of the Divino Salvador, it continued to operate as a monastery for a while, although the state owned the land and buildings.[6]

Due to its proximity to the state of Morelos, Malinalco was Zapatista territory during most of the Mexican Revolution. Malinalco put itself under the command of General Genovevo de la O starting in 1911. By 1913, Zapatistas and troops loyal to Venustiano Carranza both claimed this area. During the regime of Victoriano Huerta, Malinalco stayed loyal to the Zapatistas, despite government efforts to eradicate the rebels.[6]