Whey is the major residue generated from the industrialization of cheeses; it contains 50% of milk solids, which makes it a substrate of rapid degradation and high biochemical demand, so it is considered a high-impact contaminant.There is a high number of alternatives to use whey, e.g., implementing it directly in other process lines, fractionating it to take advantage of the properties of its components, and applying biotechnological processes. The acid whey registers a low pH that prevents it from being totally recycled, but there are still options to generate value like using it as a raw material in the elaboration of other products. Therefore, it is important to evaluate the microbiological quality of the acid whey once it is obtained. Pasteurization is considered the first action to preserve it and ensure its safety; thus, the objective of this work was to evaluate the effect of pasteurization on the microbiological quality of acid whey. The results showed that the applied heat treatment (70 °C to 73 °C for 30 seconds) reduced the microbial load for health quality indicators, but was not effective in inhibiting mesophilic aerobic and yeast counts during 27 days of storage at 2 °C. We can conclude that the pasteurization process applied to the acid whey preserved the sanitary quality by controlling microorganisms of the Enterobacteriaceae family, but the thermal parameters must be adjusted to generate the same effect on mesophilic aerobes and yeasts to fully guarantee the sanitary safety of the acid whey.