Safety and quality of compound feed for experimental animals in Costa Rica is unknown. Some contaminants, such as Salmonella spp. and mycotoxins, could elicit confounding effects in laboratory animals used for biomedical research. In this study, different batches of extruded animal feed, intended for laboratory rodents in Costa Rica, were analyzed to determine mycotoxin and microbiological contamination (i.e., Salmonella spp., Escherichia coli, total coliform bacteria, and total yeast and molds enumeration). Two methods for Salmonella decontamination (UV light and thermal treatment) were assessed. Only n = 2 of the samples were negative (representing 12.50%) for the 26 mycotoxins tested. Enniatins and fumonisins were among the most frequent toxins found (with n = 4+ hits), but the level of contamination and the type of mycotoxins depended on the supplier. None of the indicator microorganisms, nor Salmonella, were found in any of the tested batches, and no mold contamination, nor Salmonella growth, occurs during storage (i.e., 2–6 months under laboratory conditions). However, mycotoxins, such as enniatins and fumonisins tend to decrease after the fourth month of storage, and Salmonella exhibited a lifespan of 64 days at 17 °C even in the presence of UV light. The D-values for Salmonella were between 65.58 ± 2.95 (65 °C) and 6.21 ± 0.11 (80 °C) min, and the thermal destruction time (z-value) was calculated at 15.62 °C. Results from this study suggest that laboratory rodents may be at risk of contamination from animal feed that could significantly affect the outcomes of biomedical experiments. Thus, improved quality controls and handling protocols for the product are suggested.