The invention relates to the field of nutritional ingredients, in particular to economically attractive methods for producing hypoallergenic galactooligosaccharides (HA-GOS) and the use thereof in food and feed items. Provided is a method for the production of a HA-GOS preparation, comprising contacting a lactose feed with a beta-galactosidase (EC 3.2.1.23) comprising an amino acid sequence according to any of SEQ ID NO: 1, 2, 3 or 4, or an amino acid sequence that is at least 80% identical thereto, wherein the lactose feed is a cheese whey permeate (CWP) or a CWP that is enriched in sialyllactose (SL-CWP).