Introduction. Pulque is a traditional Mexican beverage made from Agave sap, involving complex microbial communities. This study used omics-based approaches to identify a core microbiota present throughout the production process from agave tissue to the final beverage and assessed its temporal stability over one year in Huitzilac, Morelos. Methodology. A total of 90 biological samples were analyzed, including triplicates of agave tissue, aguamiel (sap), and commercial pulque at three fermentation stages (T0, T3, T6). Sequencing of the 16S rRNA (V3–V4) and ITS1 regions was performed via Illumina NovaSeq. Taxonomic assignment and diversity metrics were conducted using QIIME with SILVA and UNITE databases. Metabolites were profiled using HPLC and UPLC. Results A microbial core of eight bacterial and five fungal genera was identified. Zymomonas (~58%) and Saccharomyces (~70%) were the most abundant. Core stability over the year was ~70%. Conserved genera were associated with sugar hydrolysis, metabolite production, and aroma biosynthesis. Sucrose (52 g/L), fructose (12 g/L), and glucose (17 g/L) were detected as carbon sources. Ethanol (30 g/L), and organic acids (average 4.0 g/L) increased in later stages (pulque T6), while early stages (aguamiel) were richer in carbohydrates. Conclusion. A stable and functionally relevant microbial core persists throughout pulque fermentation.