The objective of this study was to compare microfiltered native whey protein concentrate and traditional cheese whey protein concentrate powders and their functional properties. Solubility, viscosity, gelation, foaming properties, emulsification and water‐holding capacity were studied. The effect of spray and freeze drying methods on functional properties was evaluated. Gel strength varied from 0.11 to 0.65 N. Foaming stability and overrun varied from 0 to 29.3 min and from 230 to 2200%, respectively. Foaming and gelation properties were clearly better with native whey protein powders. Differences between drying methods were not observed but higher heat load decreased solubility.