Whey permeate was used as a co-substrate to replace part of the wheat for ethanol production by Saccharomyces cerevisiae. The simultaneous saccharification and fermentation was achieved with β-galactosidase added at the onset of the fermentation to promote whey lactose hydrolysis. Aspergillus oryzae and Kluyveromyces lactis β-galactosidases were two enzymes selected and used in the co-fermentation of wheat and whey permeate for the comparison of their effectiveness on lactose hydrolysis. The possibility of co-fermentations in both STARGEN and jet cooking systems was investigated in 5L bioreactors. Ethanol yields from the co-fermentations of wheat and whey permeate were evaluated. It was found that A. oryzae β-galactosidase was more efficient for lactose hydrolysis during the co-fermentation and that whey permeate supplementation can contribute to ethanol yield in co-fermentations with wheat.