Industrial development of microalgae biomass valorization relies on process optimization and controlled scale-up. Both need robust modeling: (i) for biomass production and (ii) for integrated processes in the downstream processing (DSP). Cell disruption and primary fractionation are key steps in DSP. In this study, a kinetic model, including microalgal cell size distribution, was developed for Chlorella sorokiniana disruption in continuous bead milling. Glass beads of 0.4 mm size at impeller tip velocity of 14 m.s(-1) were used as optimal conditions for efficient cell disruption. These conditions allowed faster disruption of big cells than small ones. A modified expression of the Stress Number, including cell size effect, was then proposed and validated. Separation of starch, proteins and chlorophyll by mild centrifugation was studied as function of the disruption parameters. Low energy consumption conditions led to extreme comminution. An intermediate zone drew attention for allowing moderate energy consumption and efficient metabolites separation by centrifugation.