Soft drinks are food matrices propitious to the growth of acidophilic bacteria, yeasts, and filamentous fungi due to their pH, water activity, and the presence of nutrients. Off-flavor, clouding, and package stuffing are the only parameters producers have to detect spoilage when it is often too late for the brand's reputation. In this work, microbiological analyses were performed on non-alcoholic beverages of Brazilian and Bolivian brands. As a result, Gram-positive, Gram-negative, yeast, and filamentous fungi were isolated. Zygosaccharomyces bisporus yeast was isolated from different flavored stuffed products, and Gluconacetobacter liquefaciens and Brevibacillus agri were isolated from packages without visible signs of deterioration. These microorganisms were identified by MALDI-TOF. For products with visible growth of filamentous fungi, microscopic identification keys identified Aspergillus flavus, Penicillium citrinum, Paecilomyces niveus, and Paecilomyces variotii. These work's findings reflect a failure to sanitize raw materials since the isolates' primary origin is the soil and the water, pointing to the lack of process control in soft drinks.