This work aimed at analyzing the effect of microfiltration conditions (cross-flow velocity and transmembrane pressure) on the quality of frozen Lactobacillus bulgaricus CFL1 starters produced on pilot scale. Microfiltered cells were less resistant during the concentration process than centrifuged cells. In contrast, bacterial cryotolerance during freezing was improved after microfiltration, in a range of 28-88%, depending on the microfiltration conditions. During frozen storage, cell resistance was also affected by microfiltration conditions, either positively or negatively, compared to centrifugation. The best cryotolerance was obtained for cells microfiltered at a cross-flow velocity of 2 m/s and a transmembrane pressure of 0.15 MPa. This improvement was explained by considering membrane fatty acid composition of Lb. bulgaricus CFL1. This condition increased unsaturated to saturated and cyclic to saturated fatty acid ratios, which enhanced membrane fluidity, thus helping the cells to better resist freezing and frozen storage.