In the present study, a high performance, tough, antimicrobial, hyperbranched epoxy nanocomposite is fabricated by the incorporation of neem oil-immobilized organo-modified montmorillonite nanoclay. The immobilization of neem oil with organo-modified montmorillonite nanoclay is performed by the combined effect of mechanical and ultrasonic forces under ambient conditions. This immobilization is confirmed by FTIR and XRD studies. FTIR, XRD, SEM and TEM analyses also confirm the formation of the exfoliated nanocomposite. The dose-dependent enhancements of tensile strength (50%), elongation at break (3-fold), toughness (5.5-fold) and thermal stability (20 °C) of the pristine epoxy thermoset are observed for the nanocomposite. Antimicrobial studies are performed by growth curve and zone-of-inhibition analyses against different bacteria and a fungus at different doses of neem oil-immobilized organo-modified montmorillonite nanoclay. The nanocomposite with 50 wt% neem oil-immobilized organo-modified montmorillonite nanoclay (2.5 wt%) shows significant activity against biofilm formation compared to the pristine thermoset. Thus, the studied nanocomposite has strong potential as a high-performance functional material.