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Cheese whey is a rich source of nutraceutical compounds, and little is known about how long-term preservation affects its microbial profile, physicochemical characteristics, and possible toxicity to important organs. Therefore, the microbial composition, pH, titratable acidity, and sub-chronic toxicity (in adult albino rats) of fermented cheese whey were investigated in this work during 28 days of storage. However, Staphylococcus aureus, Lactobacillus species, Micrococcus species, and S. epidermidis were the most common bacteria found in laboratory-fermented whey, which had low bacterial counts (1.7 × 10³ CFU/ml) and no fungi. Locally-fermented whey on the other hand, had significantly higher microbial loads (2.3 × 10³ CFU/ml bacteria and 9.0 × 10³ CFU/ml fungi), which also included a number of known pathogens and spoilage organisms. The fermented cheese whey acidified during storage: laboratory-fermented whey changed more slowly (pH 4.0-3.52; acidity 0.28%-0.35%), whereas locally-fermented whey showed a quicker pH drop (4.11-3.17) and increase in titratable acidity (0.29%-0.39%). Nevertheless, at day 14 no effect on the liver or kidneys but day 28, showed dose-dependent toxicity, in both fermented whey. We found that long preservation of cheese whey leads to toxicity in our in-vivo model.