The present research focuses on synthesizing selenium nanoparticles (Se NPs) coated with Methionine and Folic acid. selenium-methionine-folate nanoparticles (Se-Met-Fa NPs) were prepared by the chemical precipitation method. These were characterized by UV–Vis spectroscopy, FTIR, X-ray diffraction, Zeta potential, ICP-AES, TEM, and Raman spectroscopy. The average diameter of nanoparticles was determined by TEM was 50 nm. In Vitro viability of cells exposed to Se-Met-Fa NPs were studied using MTT and AO/EB assay. Approximately 80% of cells were viable at 100 μg/ml concentration after 24 h of incubation, suggestive of the safety of nanoparticles. Macromolecular interaction studies were carried out with plasmid DNA and Bovine serum albumin (BSA) protein. UV–Vis Spectroscopy showed ground state complex formation of Se-Met-Fa NPs with BSA. Intrinsic fluorescence of BSA was quenched by Se-met-Fa NPs via Static quenching and was observed under Spectro-fluorimetry. Conformational structural change in α-Helices of BSA was observed to be 4.4% after the interaction with Se-Met-Fa NPs, and it was studied using CD spectroscopy. At 250 μg/ml Se-Met-Fa NPs prevented oxidative damage of Plasmid DNA. The total antioxidant property of Se-Met-Fa NPs expressed in terms of scavenging of free DPPH radicals. Ten micrograms per milliliter could inhibit 41% of DPPH, proving its scavenger role at the lowest concentration. Nanoparticles comprising antioxidant semi-conducting cores and encapsulated by biomaterials that are highly bioavailable can be promising therapeutic agents for inflammation and oxidative stress disorders studies.