One of the most critical stages of conversion of agricultural waste biomass into biofuels employs hydrolysis reactions between highly specific enzymes and matching substrates (e.g. corn stover cellulose with cellulase) that produce soluble sugars, which then could be converted into ethanol. Despite numerous advantages, a major limitation of enzymatic bio-processing is relatively slow reaction rates. Our research found that the introduction of a low energy, uniform ultrasound field into enzyme processing solutions greatly improved their effectiveness by significantly increasing their reaction rate. It has been established that the following specific features of combined enzyme/ultrasound bio-processing are critically important: a) the effect of cavitation is several hundred times greater in heterogeneous systems (solid-liquid) than in homogeneous, b) in water, maximum effects of cavitation occur at ~50 ⁰C, which is the optimum temperature for many enzymes, c) cavitation effects caused by ultrasound greatly enhance the transport of enzyme macromolecules toward substrate surface and, d) mechanical impacts, produced by collapse of cavitation bubbles, provide an important benefit of “opening up” the surface of substrates to the action of enzymes. It appears that the introduction of ultrasound energy during enzymatic bio-processing of agricultural waste biomass could significantly accelerate this process and make it more suitable for widespread industrial implementation.