The utilisation of quinoa protein concentrates (QPCs) is limited due to their poor protein digestibility (78.54 %). In this study, QPCs (1 % w/v) were fermented in 5 % (v/v) water kefir grains (WKG) for 5 days at 25 °C. The protein quality of the fermented QPCs was enhanced, whereby the protein digestibility increased significantly (P < 0.05) from 78.54 to 87.67 % after 5 days of fermentation and significant (P < 0.05) changes to the secondary protein structure components (α-helix and random coil). Concurrently, saponins content and pH decreased significantly (P < 0.05). After 2 days of fermentation, the total phenolic content increased significantly (P < 0.05) from 314.5 to 528.8 mg of GAE/100 g. Various phenolic compounds were detected, with epicatechin being the most abundant in the fermented QPCs. WKG fermentation posed as a potential reliable method for enhancing the quality and protein structure of QPCs.