Microalgae are promising feedstock for biodiesel production due to their lipid content. Rotating-disk dynamic microfiltration was used for microalgae concentration in this study. The effects of operating conditions, namely disk rotation speed, suspension feed rate, and transmembrane pressure (TMP), on the filtration flux and cake properties are discussed. Because all microalgae cells were rejected by the filter membrane, the main cause of filtration resistance was highly compressible cake that exhibited a compressibility factor of 0.66. An increase in the disk rotation speed led to 40–300% increase in pseudosteady filtration flux. Applying a high TMP yielded high filtration flux at a low disk rotation speed. However, the opposite result was obtained at a high rotation speed. Nearly the same filtration fluxes were produced at a disk rotation speed of 300 rpm even when the TMPs were different. The flow fields in the rotating-disk dynamic microfilter were simulated using software of computational fluid dynamics, Fluent. The shear stress at the membrane surface is a major factor affecting cake formation. A two order-of-magnitude increase in the shear stress by increasing the disk rotation speed will decrease the cake mass by 80% and enhance the filtration flux to about 10 times in the conditions of this study. A linear relationship between mean cake mass and the ratio of filtration flux to mean shear stress derived from the force balance model was verified using experimental data measured in various operating conditions. The methods proposed by this study provide a way to estimate the cake mass and filtration flux directly from operating conditions.