Novel hierarchically-organized magnetic microspheres have been successfully developed that consist of an aqueous hollow core, a magnetic porous Fe3O4-carbon layer and a well-define hydroxyapatite (HAp) shell. The hollow magnetic carbon microspheres were prepared by ultrasonic spray pyrolysis and coated with HAp using a biomimetic approach. The resulting powders exhibit micro- and meso-porosity. The removal capacity of the composite spheres towards an antibiotic (ampicilin), a rare-earth ion (La3+) and two heavy metals (Hg2+ and Pb2+) has been studied and compared with that of the individual components. The dual organic-inorganic affinity of the magnetic HAp/carbon conjugates was demonstrated, with synergetic effects being evidenced for heavy metal removal enlightening their potentialities in wastewater treatment.