Nanoparticles (NPs) are gaining special interest due to their recent applications as antimicrobial agents to defeat the massive threat of resistant pathogens. This study focused on the utilisation of isolate S12 purified from waste discharge soil in the biological synthesis of silver (Ag), selenium (Se), and zinc oxide (ZnO) NPs. The isolate S12 was related to according to 16S rRNA sequence analysis, morphological characteristics, and biochemical reactions. The cell-free supernatant has been used for the synthesis of Ag, Se, and ZnO NPs. The synthesised NPs were characterised using ultraviolet-visible spectroscopy, dynamic light scattering (DLS), transmission electron microscopy, and Fourier transform infrared spectroscopy. The biogenic NPs were evaluated for antimicrobial effects against different Gram-positive and Gram-negative resistant isolates using the broth microdilution method. They showed antibacterial effect against standard and resistant isolates; , ATCC 29213, S1.1, methicillin resistant (MRSA 303, 402 and 807), ATCC 12435, E7, ATCC 51503, K5, K112, PAO1, and P8. This study showed the green synthesis of various NPs using isolate S12 which demonstrated diverse activities against multi-drug resistant isolates.