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The aim of this study was to assess the inhibitory effect of three commercial bioprotectant agents on the growth of yogurt-spoiling fungi. Mucor circinelloides, Mucor racemosus, Penicillium spp., Saccharomyces exiguus, and Candida intermedia, commonly involved in the spoilage of dairy products, were isolated from spoiled yogurt and were fully characterized using molecular and phenotypic methods. HOLDBAC-YMC™, Lyofast-FPR2™ and MicroGARD 200™ were used as antifungal products. An optimized experimental mixture design was applied to determine the proportion of each bioprotectant in terms of growth-inhibition response against the fungal strains in standard laboratory media. The results of the challenge tests showed that the application of bioprotectants inhibited the growth of the moulds in the range of 85–100% and the growth of yeast between 1.23 and 5.40 log cycles. The optimal combination of the bioprotectants was determined, tested in standard laboratory media and found to inhibit fungal growth. The antifungal effect of the optimal combination of the bioprotectants was validated in yogurt against the most resistant fungal species of the study, M. circinelloides and C. intermedia. The bioprotectants elicited antifungal effect in yogurt by completely inhibiting all of the tested fungi compared to controls. To the best of our knowledge, this is the first time a mixture of commercial bioprotectants has been tested on yogurt as a potential alternative for the biopreservation of yogurt in order to reduce spoilage of fermented dairy products and economic losses.