Lemon pectin extracted along with water-soluble flavonoids and other phytochemicals from citrus industry’s waste lemon peel via hydrodynamic cavitation in water, directly at pre-industrial scale and further isolated via freeze drying, shows exceptionally high antioxidant and non-cytotoxic activity. Preliminary investigation indicates also significant antimicrobial activity. These findings open the route to the development of new nutraceutical and healthcare application of a versatile biopolymer endowed with new functionality, rapidly and conveniently obtained from an abundant by-product of the agrofood industry.