During low-pressure membrane treatments of cyanobacterial cells, including microfiltration (MF) and ultrafiltration (UF), there have reportedly been releases of intracellular compounds including cyanotoxins and compounds with an earthy-musty odor into the water, probably owing to cyanobacterial cell breakage retained on the membrane. However, to our knowledge, no information was reported regarding the effect of growth phase of cyanobacterial cells on the release of the intracellular compounds. In the present study, we used a geosmin-producing cyanobacterium, Anabaena smithii, to investigate the effect of the growth phase of the cyanobacterium on the release of intracellular geosmin during laboratory-scale MF experiments with the cells in either the logarithmic growth or stationary phase. Separate detection of damaged and intact cells revealed that the extent of cell breakage on the MF membrane was almost the same for logarithmic growth and stationary phase cells. However, whereas the geosmin concentration in the MF permeate increased after 3 h of filtration with cells in the logarithmic growth phase, it did not increase during filtration with cells in the stationary phase: the trend in the geosmin concentration in the MF permeate with time was much different between the logarithmic growth and stationary phases. Adsorption of geosmin to algogenic organic matter (AOM) retained on the MF membrane and/or pore blocking with the AOM were greater when the cells were in the stationary phase versus the logarithmic growth phase, the result being a decrease in the apparent release of intracellular geosmin from the stationary phase cells. In actual drinking water treatment plants employing membrane processes, more attention should be paid to the cyanobacterial cells in logarithmic growth phase than in stationary phase from a viewpoint of preventing the leakage of intracellular earthy-musty odor compounds to finished water.