Galacto-oligosaccharides (GOS) are prevalent prebiotic ingredients of various functional foods. GOS synthesis by β-galactosidase from whey-derived lactose results in a crude GOS mixture containing additionally lactose, glucose and galactose. In this study, we assessed the potential of lactic acid bacteria for depleting non-GOS sugars from crude GOS by selective fermentation. We aimed to combine the prebiotic characteristics of purified GOS with the health promoting effects of lactic acid fermentation metabolites. Our results indicated that supplementation of crude GOS with casein hydrolysate and retardation of acidification during fermentation stimulated cell growth, mono- and disaccharide consumption, overall organic acid production and diversity of the produced acids. Fermentation performed by Lactobacillus paracasei PB9 and L. plantarum 2108 resulted in lactic and citric acid containing high purity GOS media with a final pH below 4.6. We assessed the products as nutritionally safe that open a way to the formulation of prebiotic fermented beverages. Moreover, lactic fermentation of crude GOS would offer an alternative to the end-to-end valorization of whey-derived lactose.