Described herein are methods for preparing isomaltooligosaccharides (“IMOs”) from a carbohydrate substrate and uses thereof. In the presence of a maltogenic enzyme and additional IMO precursors, an Aspergillus sp. invertase is capable of producing IMOs from a starch slurry. The ability of the invertase to function as a transglucosidase enzyme imparts a simultaneous mechanism for IMO saccharification.