Nanoparticles of selenium and gold when synthesized through the green route using aqueous plant extract, exhibit strong antimicrobial activities with minimum or no toxicity. Aegle marmelos (L) Correa, an ethnobotanically well-known fruit for its wide medicinal values, has been utilized in this work for the synthesis of both, selenium and gold nanoparticles. The synthesis of the nanoparticles was first detected by the change in colour and formation of colloids in the reaction solution, followed by UV–visible spectroscopy. The λmax of selenium and gold nanoparticles were found at 333 nm and 552 nm, respectively. The XRD spectrum confirms the pure crystalline nature of the nanoparticles. Scanning electron microscopic image revealed their shape as mostly spherical, however, few of the gold nanoparticles were found to be triangular. Both the nanoparticles have shown significantly strong antibacterial activity against the tested pathogens (Micrococcus luteus, Klebsiella pneumoniae, Staphylococcus epidermidis, Pseudomonas aeruginosa, and Staphylococcus aureus) and the best activity has been observed in S. epidermidis for both SeNP and AuNP. © 2022, The Author(s) under exclusive licence to Society for Plant Research.