In recent years, microfiltration (MF) has gained great interest as an excellent technique for clarification of biological suspensions. This paper addresses a direct comparison of efficiency, performance and susceptibility to cleaning of the ceramic and polymeric MF membranes applied for purification of 1,3-propanediol (1,3-PD) fermentation broths and suspensions of yeast Saccharomyces cerevisiae. For this purpose, ceramic, titanium dioxide (TiO2) based membranes and polypropylene (PP) membranes were used. It has been found that both TiO2 and PP membranes provide sterile permeate during filtration of 1,3-PD broths. However, the ceramic membrane, due to the smaller pore diameter, allowed obtaining a better quality permeate. All the membranes used were highly susceptible to fouling with the components of the clarified broths and yeast suspensions. The significant impact of the feed flow velocity and fermentation broth composition on the relative permeate flux has been demonstrated. Suitable cleaning agents with selected concentration and duration of action effectively cleaned the ceramic membrane. In turn, the use of aggressive cleaning solutions led to degradation of the PP membranes matrix. Findings of this study add to a growing body of literature on the use of ceramic and polypropylene MF membranes for the clarification of biological suspensions.