Seven lactobacilli and a variety of microflora extracted from twenty five commercial cheeses were grown on unsupplemented acid goat whey and screened for their capacity to hydrolyse whey proteins [α-lactalbumin (α-la) and β-lactoglobulin (β-lg)] and to generate peptides. Fermentations were performed aerobically or anaerobically at 37 °C using crude or pre-heated whey (10 min at 65, 75 or 85 °C). Under aerobic conditions, growth of lactobacilli was poor and protein hydrolysis did not occur. Anaerobic conditions slightly increased lactobacilli growth but neither β-lg hydrolysis nor peptide generation were observed. More than 50% of α-la was digested into a truncated form of α-la (±12 kDa) in crude whey and whey pre-heated at 65 °C. Twenty-five microflora extracted from raw milk cheeses were screened for their proteolytic activities on acid goat whey under the conditions previously described. Eight of them were able to hydrolyse up to 50% of α-la mainly during aerobic growth on crude or pre-heated whey. The corresponding hydrolysates were enriched in peptides. The hydrolysate involving microflora extracted from Comté cheese after or at 18 months ripening was the only one to exhibit hydrolysis of both α-la and β-lg. Microbiological analysis showed that microorganisms originating from Comté cheese and capable of growth on unsupplemented whey consisted of Candida parapsilosis and Lactobacillus paracasei. Fermentation kinetic profiles suggested that peptides were released from α-la hydrolysis. The co-culture of both microorganisms was required for α-la hydrolysis that occurred concomitantly with the pH decrease. During whey fermentation, Cand. parapsilosis excrete at least one protease responsible for α-la hydrolysis, and Lb. paracasei is responsible for medium acidification that is required for protease activation.