In this work, we present a novel type of magnetic-fluorescent bifunctional nanoparticle (NP). Fe₃O₄ nanocrystals and cationic fluorescent star polymer perylene diimide–poly(2-aminoethyl methacrylate) (PDI–PAEMA) were simultaneously encapsulated into a silica matrix by a one-pot method. The morphology and fluorescence properties of Fe₃O₄/PDI–PAEMA@SiO₂ core–shell NPs were investigated by ultraviolet-visible (UV-vis) spectrometry, fluorescence spectrometry and high resolution transmission electron microscopy (HRTEM). The analysis of in vitro intracellular uptake and cell viability revealed that the bifunctional NPs possessed favourable biocompatibility. Taken together, the Fe₃O₄/PDI–PAEMA@SiO₂ NPs could be a promising candidate for bioimaging due to their stable red emission and favourable biocompatibility.