In this study, the parameters for the adsorption of indigo blue dye onto iron oxide nanoparticles were optimized in a batch system (Fe3O4@ME nanoparticles nanomaterials synthesized using bacterial extracts and Fe3O4 nanomaterials synthesized using bacterial cell mass). The Taguchi optimization approach (an L9 array design) was utilized to estimate the significance and interaction impacts of many examined parameters (initial concentration of indigo blue dye, adsorbent dose, and contact time) on the adsorption process. It was observed that the ideal conditions were 0.125 gm of adsorbent, 13 mg/lit of initial dye concentration, and 90 minutes of contact time at pH 7, room temperature. In this study, at optimized conditions, the percent dye removal for Fe3O4 and Fe3O4@ME nanoparticles was 86 and 76, respectively. The percentage contribution of each process parameter to the elimination of indigo blue dye was determined using the Analysis of Variance (ANOVA) method. It was found that Taguchi could accurately forecast the outcomes. In order to support the accuracy of the process parameter optimization under the specified experimental conditions, it was found that the percentage removal of the indigo blue dye obtained in the confirmatory experiments carried out under optimized conditions was higher than that optimized in each of the Taguchi design's test runs.