The intensification of processes is essential for the sustainability of the biorefinery concept. Enzyme catalysis assisted by ultrasound (US) may offer interesting opportunities in the agri-food sector because the cavitation effect provided by this technology has been shown to improve the efficiency of the biocatalysts. This review presents the recent advances in this field, focused on three main applications: ultrasound-assisted enzymatic extractions (UAEE), US hydrolysis reactions, and synthesis reactions assisted by US for the manufacturing of agri-food produce and ingredients, enabling the upgrading of agro-industrial waste. Some theoretical and experimental aspects of US that must be considered are also reviewed. Ultrasonic intensity (UI) is the main parameter affecting the catalytic activity of enzymes, but a lack of standardization for its quantification makes it unsuitable to properly compare results. Applications of enzyme catalysis assisted by US in agri-foods have been mostly concentrated in UAEE of bioactive compounds. In second place, US hydrolysis reactions have been applied for juice and beverage manufacturing, with some interesting applications for producing bioactive peptides. In last place, a few efforts have been performed regarding synthesis reactions, mainly through trans and esterification to produce structured lipids and sugar esters, while incipient applications for the synthesis of oligosaccharides show promising results. In most cases, US has improved the reaction yield, but much information is lacking on how different sonication conditions affect kinetic parameters. Future research should be performed under a multidisciplinary approach for better comprehension of a very complex phenomenon that occurs in very short time periods.