<p>This paper describes a new modeling methodology destined to develop a mathematical model of a bioreactor used in the bacterial oxidation process. Based on the literature review, a comparative analysis was carried out with the existing model. To customize the parameters in the bioreactor, the coefficients of the fuzzy PID controller were adjusted based on specified settings. The effectiveness of the suggested method is proven by comparing other available methods designed for tuning controllers that described in the literature. The research findings show that the proposed method is highly effective with rational regulation of bioreactor parameters. Moreover, the given method was tested in the nonlinear state of the bioreactor’ model for presence of noise within the process of measurement.</p>