Chikungunya, dengue, Zika, malaria, Japanese encephalitis, filariasis, West Nile, etc. are mosquito transmitted diseases that have killed millions of people worldwide, and millions of people are at risk of these diseases. Control of the mosquitoes, such as Aedes aegypti and Culex quinquefasciatus, is challenging due to their development of resistance to synthetic insecticides. The habitats of the young mosquitoes are also the habitats for foodborne pathogens like Staphylococcus aureus (MTCC96) and Serratia marcescens (MTCC4822). The present study was aimed at synthesizing eco-friendly green nanoparticles using Dillenia indica leaf broth and analyzing its efficacy in controlling the vector mosquitoes A. aegypti and C. quinquefasciatus, as well as the microbial pathogens St. aureus and Se. marcescens. The formation of selenium nanoparticles (SeNps) was confirmed using UV-Vis spectroscopy (absorption peak at 383.00 nm), Fourier transform infrared radiation (FTIR spectrum peaks at 3177, 2114, 1614, 1502, 1340, 1097, 901, 705, and 508 cm−1), X-ray diffraction (diffraction peaks at 23.3 (100), 29.6 (101), 43.5 (012), and 50.05 (201)), and scanning electron microscopy (oval shaped). The size of the nanoparticles and their stability were analyzed using dynamic light scattering (Z-Average value of 248.0 nm) and zeta potential (−13.2 mV). The SeNps disorganized the epithelial layers and have broken the peritrophic membrane. Histopathological changes were also observed in the midgut and caeca regions of the SeNPs treated A. aegypti and C. quinquefasciatus larvae. The SeNps were also active on both the bacterial species showing strong inhibitory zones. The present results will explain the ability of SeNps in controlling the mosquitoes as well as the bacteria and will contribute to the development of multi potent eco-friendly compounds.