The aim of this study was to evaluate thermosonication as an alternative method for the pasteurization of pulque in order to improve its shelf life and retain its quality parameters.Thermosonication was carried out at 50 °C using amplitudes of 75% (for 6 and for 9 min), 85% (for 4 and for 6 min), and 95% (for 3 and for 5 min). These were the optimal conditions found for processing pulque by thermosonication. Physicochemical (acidity, color, alcohol content, and sensory analysis) and microbiological (lactic acid bacteria and yeasts) parameters were determined during 30 days for storage at 4 ± 1 °C. Conventional pasteurization (63 °C, 30 min) and raw pulque were used as controls. According to the results, the shelf life of pulque was extended up to 24 days storage at 4 °C. After this time, the quality of beverage decreased, due that the microbial load increases. Thermosonication treatments at 75% and 85% showed a higher content of LAB (6.58–6.77 log CFU/mL) and yeasts (7.08–7.27 log CFU/mL) than conventional pasteurization (3.64 log CFU/mL of LAB and 3.97 log CFU/mL of yeasts) at 24 days of storage. Raw pulque demonstrated up to 7.77 log CFU/mL of yeasts and 7.51 log CFU/mL of LAB. Pulque processed by thermosonication exhibited greater lightness, sensory acceptance, a maximal acidity of 0.83 g/lactic acid, and an alcohol content of 4.48–4.95% v/v. The thermosonication process preserves sensory and physicochemical properties better than conventional pasteurization. Lactic acid bacteria such as Lactobacillus kefiri, Lactobacillus acidophilus, and Lactobacillus hilgardii and yeasts such as Saccharomyces cereviasiae were identified in thermosonicated pulque.