In this work a fouling study of polypropylene membranes used for microfiltration of glycerol solutions fermented by Citrobacter freundii bacteria was presented. The permeate free of C. freundii bacteria and having a turbidity in the range of 0.72–1.46 NTU was obtained. However, the initial permeate flux (100–110 L/m2h at 30 kPa of transmembrane pressure) was decreased 3–5 fold during 2–3 h of process duration. The performed scanning electron microscope observations confirmed that the filtered bacteria and suspensions present in the broth formed a cake layer on the membrane surface. A method of periodical module rinsing was used for restriction of the fouling influence on a flux decline. Rinsing with water removed most of the bacteria from the membrane surface, but did not permit to restore the initial permeate flux. It was confirmed that the irreversible fouling was dominated during broth filtration. The formed deposit was removed using a 1 wt% solution of sodium hydroxide as a rinsing solution.