This area is believed to have been conquered by the Aztecs during the 1470s, but the House of the Eagles is believed to have been constructed in the early 1500s. Archeologists surmise that the site was built on top of the abandoned ruins of a much older settlement of Toltec or Teotihuacan origin, probably to mythologize and therefore legitimize Aztec rule as heirs.

Malinalco was significant to the Aztecs because it held a deep association with the goddess of witchcraft and black magic, Malinalxóchitl. The archaeological site has six buildings, but the most impressive one is the House of the Eagles, which consists of a small stone walled and thatched roofed that has been reconstructed based on historical accounts. It stands atop a staired pyramid platform.

At the foot of the stairs stands a stone sculpture of a jaguar that is sadly now headless, while within the house are three fearsome eagle sculptures and a single well-preserved jaguar that bares its fangs and outstretched claws. Several sacred stone bowls are situated around the interior of the house and are believed to have once been used to place the hearts of sacrificial victims who may have been killed here. Murals once apparently covered the walls, but unfortunately, these deteriorated and have vanished.

During the Aztec reign, the primary purpose of the House of the Eagles was to be a sanctuary for the elite Eagle and Jaguar Warriors to retreat here between battles to train in warfare tactics and perform sacred rituals associated with witchcraft. Later in its history, the town was the setting for several small battles between the conquistadors and the last surviving Aztec warriors of Tenochtitlan (present-day Mexico City ) during the Spanish conquest of Mexico. However, resistance was soon crushed and the town was defeated, falling under the power of the Spanish crown.