Aqueous two-phase system (ATPS) composed of polyethylene glycol (PEG) and K2HPO4 solutions was used to extract saponin from sugar beet root. Extraction yield, purity and foam capacity of saponin were optimized according to response surface methodology (RSM). Analysis of liquid chromatography-mass spectrometry (LC-MS) showed that purified saponins were composed of hederagenin, akebonoic acid and oleanolic acid. Addition of 0.02 g sugar beet root saponin to one liter of malt beverage caused a considerable increase in foam volume and stability compared to malt beverage samples containing 0.1 g/L propylene glycol alginate (PGA). Malt beverages containing saponin showed higher turbidity, bitterness and overall sensory acceptance. Moreover, no significant changes in malt drink pH and °Brix were observed due to saponin addition. Adding lemon flavor caused a decrease in foam stability and sensory acceptance of malt beverage containing saponin compared to PGA containing ones. Less saponin content is suggested for flavored malt drinks. The online version contains supplementary material available at 10.1007/s13197-022-05517-x.