Pulque is a beverage that has been prepared in Mexico since pre-Hispanic times from the fermented sap of more than 30 species of wild and domesticated agaves. We conducted studies in two communities of the state of Michoacán, in central-western Mexico, where we documented its traditional preparation and analyzed the relationship between preparation conditions and the composition and dynamics of microbiological communities, as well as the physical and chemical characteristics of the beverage. In one of the communities, Santiago Undameo (SU), people boil the sap before inoculating it with pulque inoculum; this action causes this local pulque to be sweeter, less acidic, and poorer in bacteria and yeast diversity than in the other community, Tarimbaro (T), where the agave sap is not boiled and where the pulque has more diversity of microorganisms than in SU. Fermentation management, particularly boiling of the agave sap, influences the dynamics and diversity of microbial communities in the beverage.