In this work the fouling of polypropylene membranes during the membrane distillation used for the separation of fermentation broth was studied. The glycerol fermentation was carried out using the following bacteria: Lactobacillus casei, Lactococcus lactis and Leuconostoc mesenteroides. During the process operation a large amount of biomass was deposited on the surface of membranes immersed in the broth, causing a decline of the permeate flux by 50%. The majority of precipitate was removed using a multiple rinsing of the membranes with water, which restored the initial yield of the MD modules. Nutrients used for the preparation of broth (glycerol, peptone K and yeast extract) did not cause the membrane fouling. The used membranes did not undergo the wettability and a high degree of separation was maintained for 1000h of membrane bioreactor operation. The application of membrane distillation allowed to separate the acetic acid from fermentation broth, which improved the conditions of bacterial growth. Effect of biofouling on permeate flux drop membrane refining of glycerol solutions fermented by bacteria was studied. The changes of the polypropylene membrane retention during the long-term MD study were presented. The application of membrane distillation allowed to separate the acetic acid from fermentation broth.