This research work aimed to isolate and culture the bacterium Bacillus paramycoides for biogenic fabrication of zinc oxide nanoparticles, specifically ZnO and ZnO-ME nanoparticles (nanoparticles fabricated from bacterial extracts only - ZnO, and from bacterial cell mass including extract - ZnO-ME). SEM investigation revealed the spherical-shaped NPs with 22.33 and 39 nm in size for ZnO and ZnO-ME, respectively. The Brunauer, Emmett, and Teller (BET) studies revealed mesoporous structure with pore diameters of 13.839 and 13.88 nm and surface area of 7.617 and 33.635 m2/gm for ZnO and ZnO-ME, respectively. Various parameters for the adsorption of sulfur black dye onto both ZnO and ZnO-ME were screened and optimized using Plackett-Burman Design (PBD), Full Factorial Design (FFD) and Central Composite Design (CCD). The results of the optimization modeling study revealed that FFD yielded the most predictable and best-fitting results among all the models studied, with R2 values of 0.998 for ZnO and 0.993 for ZnO-ME. Notably, ZnO-ME exhibited a greater dye removal efficiency 80% than ZnO i.e., 71%, it may be due to the presence of amorphous carbon on the surface of ZnO-ME. Among the various isothermal models, the Freundlich model displayed the strongest correlation with the dye removal data, confirming the multilayer adsorption of dye on both nanoparticles and supporting physisorption. Therefore, ZnO and ZnO-ME nanoparticles have been proven as potential tools for mitigating environmental impacts associated with dye-containing wastewater.