The effect of the fermentation carbon source on microfiltration of Corynebacterium glutamicum (C. glutamicum) was investigated. We previously reported that the specific resistance during the dead end microfiltration was controlled by changing pH and ionic strength through changes in the surface properties of cells; specific resistance was reduced in the condition where cells are hydrophobic and less charged. The batch fermentation of C. glutamicum was conducted with two defined media with either glucose or sucrose as carbon source and a complex medium with beet molasses as the carbon source. The specific filtration resistance of the cells produced was determined after washing the cells with deionized water. At neutral pH the specific resistance of cells cultivated with sucrose was half of that of cells grown with glucose. Fermentation with complex medium resulted in much higher specific resistances. Changes in zeta potential and hydrophobicity explained the difference in specific resistance of cells cultivated with defined media, but could not account for the large increase for the complex media. Extracellular matrix on surface of these cells, observed with transmission electron microscopy, may have been the cause.