Catastrophic events (climatic, tectonic, volcanic, etc.) frequently cause geomorphological instability, which interrupts normal pedogenesis and switches the processes of surface erosion and/or sedimentation. These processes have an effect on the distribution of ancient settlements and can be the cause of the abandonment of cities. In the Lerma Valley, particularly in the Tres Mezquites area, surveys and extensive excavations have been conducted to estimate the nature and density of pre-Hispanic settlements on the alluvial plain and in the piedmonts. Most of the archaeological structures are covered by dark clayey soils (Vertisols). This includes the PA3_El Pitayo site, where an accumulation of black earth has been detected on the floors and walls of a collapsed building. We have studied in detail the Vertisols and the black earth around the site to establish to what extent this dark earth is an in situ product of the soil-forming factors, or if its accumulation is due to erosion/sedimentation processes, which could affect the occupation of the site, or the result of anthropic activity for leveling. The Vertisols and the dark earth are characterized by different means (physical, chemical, micromorphology, clay mineralogy, and radiocarbon dating). The results show that both the Vertisols and the black earth are very clayey, with angular blocky structures and slickensides (properties that are typical of vertic soils), and smectite as the main clay mineral. Besides smectite, under the microscope, a high amount of fresh volcanic glass is identified, suggesting that volcanism could be responsible for the abandonment of the study site. However, there are no known volcanic events related to the age of abandonment. As a consequence, we consider that landslides triggered by seismic activity/climatic events impacted the settlement.