Selenium nanoparticles (UP-SeNPs) were synthesized from ultrasonically extracted date seed polysaccharides (UP) using a redox reaction between sodium selenite and ascorbic acid. The UP-SeNPs were effectively characterized for their particles size and surface, elemental compositions; in-vitro digestibility and antioxidant, antimicrobial, prebiotic and gut microbiota modulating potential of the bio accessible fractions. Glucooligosaccharide (GP-NPs) and selenium SeNPs nanoparticles were prepared as controls for biological activities and fecal fermentation. The resulted UP-SeNPs were uniform, spherical, and amorphous with a stable dispersion for 42 days and an average size of 90.5 nm. Compared to native UP and selenite, UP-SeNPs displayed increased antioxidant capacities, including dose-dependent radical scavenging (89 %), DPPH (76.4 %), ABTS (83.3 %), reducing power (809.5 μg/mL), FRAP (798.7 μg/mL), and metal chelating ability (12,230 μg/mL). Additionally, UP-SeNPs exhibited superior α-amylase (74.3 %), α-glucosidase (87 %), and ACE (64 %) inhibitions potential and significant antibacterial effects against several major foodborne pathogens. Probiotic investigations demonstrated the prebiotic impact of UP-SeNPs, supporting in vitro fecal fermentation while maintaining natural gut microbiota diversity. UP-SeNPs effectively reduced the Bacillota-to-Bacteroidota ratio, limiting pathogenic microorganisms and promoting a healthier gut environment. Functional predictions highlighted upregulated metabolic pathways, including SCFA biosynthesis (acetate, propionate, and butyrate) that are essential for preventing gut dysbiosis and maintaining energy homeostasis. UP-SeNPs also improved carbohydrate metabolism and fatty acid biosynthesis, making them readily bioavailable for colonic microbiota. Overall polysaccharide conjugation with selenium nanoparticles delivered resultant NP with improved stability, functionality and bioactive potentials compared to SeNPs on their own. The conjugation was also able to further deliver UP-SeNPs that had prominent prebiotic and gut microbiota modulation potentials.