Submerged membrane bioreactors are effective tools for synergistic production of valuable compounds, cell retention in the bioreactor, and separation of products from the reaction solution. However, membrane fouling is a problem that impairs efficiency of processes involving submerged membrane bioreactors. One of the mechanical methods for efficient fouling mitigation is backwash. Therefore, this study investigated backwash as a method for mitigating biofouling in a submerged ceramic membrane bioreactor, specifically in terms of separation of Saccharomyces cerevisiae from the suspension. To identify the key factors affecting the dynamic flux and their interactions, a Fractional Factorial Design (FFD) was employed based on the key operating variables (2 levels, 5 variables). The average flux model showed a dependency on the flow rate of backwash, time between backwash cycles, backwash duration, cell concentration, and separation process time (adjusted R2 = 0.99). Furthermore, the effect of backwash on flux recovery was assessed in comparison to separation processes without backwash. It was found that after the application of backwash, up to 100 % of the initial flux could be recovered. In contrast, only around 20 % of the initial flux could be maintained after the process without backwash. The optimized conditions of backwash were found to be a flow rate of backwash at 1500 mL min−1, time between backwash cycles 5 min, backwash duration 5 sec, cell concentration 20 g dry weight per liter, and separation process time 0.5 h. The mechanism of membrane fouling was determined to be the deposition of yeast cells on the membrane surface and the blocking of pores inside the membrane by sorbitan monostearate as a reagent present in the yeast suspension.