Microalgae produce not only lipids for biodiesel production but also valuable biochemicals which are often accumulated under cellular stress mediated by certain chemicals. While the microcarriers for the application of drug delivery systems for animal cells are widely studied, their applications into microalgal research or biorefinery are rarely investigated. Here we develope dual-functional magnetic microcapsules which work not only as flocculants for microalgal harvesting but also potentially as microcarriers for the controlled release of target chemicals stimulating microalgae to enhance the accumulation of valuable chemicals. Magnetic microcapsules are synthesized by layer-by-layer(LbL) coating of PSS-PDDA on Fe3O4 nanoparticle-embedded CaCO3 microparticles followed by removing CaCO3 sacrificial templates. The positively charged magnetic microcapsules flocculate microalgae by electrostatic interaction which are sequentially collected by the magnetophoretic separation. The microcapsules with a polycationic outer layer provide efficient binding sites for negatively charged microalgae and by that means are further utilized as a chemical-delivery and flocculation system for microalgal research and biorefineries.