Magnetic collection of the microalgae Chlorella sp. from culture media facilitated by low‐gradient magnetophoretic separation is achieved in real time. A removal efficiency as high as 99% is accomplished by binding of iron oxide nanoparticles (NPs) to microalgal cells in the presence of the cationic polyelectrolyte poly(diallyldimethylammonium chloride) (PDDA) as a binder and subsequently subjecting the mixture to a NdFeB permanent magnet with surface magnetic field ≈6000 G and magnetic field gradient <80 T m−1. Surface functionalization of magnetic NPs with PDDA before exposure to Chlorella sp. is proven to be more effective in promoting higher magnetophoretic removal efficiency than the conventional procedure, in which premixing of microalgal cells with binder is carried out before the addition of NPs. Rodlike NPs are a superior candidate for enhancing the magnetophoretic separation compared to spherical NPs due to their stable magnetic moment that originates from shape anisotropy and the tendency to form large NP aggregates. Cell chaining is observed for nanorod‐tagged Chlorella sp. which eventually fosters the formation of elongated cell clusters.