The milpa is a traditional Mesoamerican polycropping system involving rain-fed cropping of maize (Zea mays), squash (Cucurbita moschata) and legumes (Phaseolus vulgaris, Phaseolus lunatus, Vigna unguiculata), crops which in this part of the world are known as the three sisters. Despite alterations due to socio-economic changes during the twentieth century, milpafarming still characterizes subsistence production systems of peasants of Maya ethnicity in the central Yucatan Peninsula, Mexico. In Dziuché, a community in the state of Quintana Roo, more ‘classical’ interpretations of the milpa, commonly cultivated by the older generation of peasants, are competing with systems that are essentially hybrids of the milpa and conventional maize farming; however, management and output of both variants are affected recently by changing precipitation patterns associated with global climate change. In the present study, implemented in Dziuché in 2012–2014, we recorded and analysed recent changes in milpa production systems. Particularly, we compared the milpas of two peasants from different generations – one is 30 years old and the other 56 years old. Through a triangulation of participatory and qualitative methodologies, including dialogue between interlocutors, focus groups, and participatory elaboration of an agricultural calendar, we recorded their perceptions of the impacts of climate change on crop management, yield and agrobiodiversity. This information was enriched with economic data related to these production systems. The data was then validated with the entire peasant assembly of Dziuché. It was observed that, regardless of their age, traditional farmers responded to the late arrival or non-arrival of the early summer rainy season by shifting their maize planting dates and by reducing agrobiodiversity, mainly by eliminating beans. The results contribute to the current discussion around the impacts of climate change on traditional production systems. It was shown that despite resilience mechanisms inherent to peasant farming, the magnitude of climate change is challenging farmers to an extent that they respond with objectively counterproductive measures, such as decreasing agrobiodiversity. It must be added that in the case of Maya peasants, these reactions are not only caused by altering climatic conditions but also by socio-economic developments like the loss of empirical knowledge transfer, a decreasing number of family members available for unpaid agricultural work, and changes in land tenure.