Effect of combined microwave (MW) and enzymatic hydrolysis on the human immunoglobulin E (IgE)-binding properties of β-lactoglobulin (β-lg) and other whey proteins (WP) was investigated. Separated β-lg and full whey protein isolate (WPI) were hydrolyzed with trypsin, chymotrypsin, mixture of trypsin/chymotrypsin, and pepsin at three microwave power levels: 50 W during 1 and 5 min, 100 and 200 W during 1 and 3 min. The immunoreactivity of the obtained hydrolysates resulting from combined microwave protease treatment was assessed using sera of young patients allergic to bovine whey proteins. The application of microwave treatment at 200 W enhances the hydrolysis of β-lg by pepsin in 3 min and decreases significantly its immunoreactivity. The extensive hydrolysis of the microwave-treated β-lg and WPI with trypsin, chymotrypsin, and the mixture of trypsin with chymotrypsin did not have an impact on the IgE binding of the products obtained in all the studied conditions.