The main objectives of this study were to investigate the possibilities of green synthesis of nanoselenium using raw and purified pectins extracted from mandarin peel, tomato pomace and olive pomace extract rich in polyphenols. The influence of different synthesis conditions on the size distribution, zeta potential and gastrointestinal stability of the obtained nanoparticles was investigated. It is possible to synthesize selenium nanoparticles with unimodal particle size distribution (104,2-147,6 nm) and satisfactory zeta potential (around -35 mV) using raw and purified pectin fractions isolated from tomato pomace and mandarin peel, while olive pomace extract can be used only in combination with encapsulating agents (polysorbate). The process of digestion significantly affects particle size distribution of nanoselenium of all investigated samples, whereby the nanoparticles agglomerate or disintegrate into smaller particles. The most stable systems with potentially good bioavailability were those encapsulated with purified pectin fraction. The results of this research significantly contribute to the existing knowledge about possibilities of using natural extracts in synthesis of metal nanoparticles and the gastrointestinal stability of nanoselenium, as well as the possibilities and justification of its use as a nutraceutical.