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ABSTRACTThis research is part of an effort to enhance fermented whey proteins’ quality and nutritional value. In this research, we investigated the feasibility of using a natural fermentation approach on whey proteins. We determined the protein digestibility, non-nutritive compounds (including phenolic compounds and saponins), and microbiological quality of water kefir-fermented whey proteins. Due to the water kefir-induced fermentation of whey proteins, the protein digestibility improved from 88.48 to 94.33%. The protein quality of fermented whey proteins has been modified after the water kefir fermentation, as observed with the changes in the secondary protein structure components, especially α-helices (decreased from 10.58 to 8.52%) and random coil (increased from 12.25 to 17.33%). In addition, their water solubility, surface hydrophobicity, and surface charge changed significantly (P < .05) during the fermentation time; 88.44 to 94.11%, 387.23 to 272.7 a.u. and −30.06 to −34.93 mV, respectively. Furthermore, water kefir is an excellent source of fermenting microorganisms, including lactic and acetic acid bacteria and yeast. Thus, the water kefir fermentation approach could be an effective, practical, non-thermal approach for altering whey proteins.