Magnetophoretic separation of Chlorella sp. microalgal biomass is proven to be a feasible downstream processing technology for biofuel production. Kinetic study of cells separation in real time reveals the major steps involved for each stage of low gradient magnetic separation (LGMS) with field gradient (del B) less than 80 T m(-1). Transmission and scanning electron microscopy (TEM & SEM) together with Fourier transforms infrared (FTIR) spectra analysis are employed to confirm the full attachment of surface functionalized iron oxide nanoparticles (SF-IONPs) onto microalgal cells and how the particles distributed on the cell's surfaces. From the cross section TEM images of cells, IONPs shown the tendency to be internalized into Chlorella sp. cells but not affect the biofuel quality.