Sporopollenin exines microcapsules, derived from the naturally occurring spores of Lycopodium clavatum, have been loaded in-situ with humic acid sodium salt-Zinc (HA-Zn) complex. The chemical treatment method utilised to prepare the sporopollenin microcapsules from raw spores was discussed and the resulted sporopollenin microcapsules were characterised using SEM, TGA and FTIR. Metal complexes of the sodium salt of humic acid and zinc ion were prepared using different protocols and in-situ loaded into the pre-treated sporopollenin microcapsules. The resulted complex was characterised before and after the encapsulation process using FTIR, TGA and XRD techniques. The morphology of the empty and loaded sporopollenin was not altered. Infrared spectroscopy revealed an increase in the absorption for COO − vibrations at 1583 and 1384 cm −1 in the FTIR spectra of HA-Zn complex compared to that of the original sodium salt of humic acid, indicative of bonding of the metal ions in hydrated form to the carboxyl or phenolic hydroxyl groups or both of the sodium humate molecules. TGA results of the HA-Zn complex loaded sporopollenin showed that around %15 of residual HA-Zn was successfully encapsulated indicative of the efficiency of the protocol used. We showed also that biodegradable magnetite nanoparticles can be surface modified with HA and encapsulated into sporopollenin. The resulted biosorbents microcapsules can be used for enhanced magnetic removal of either heavy metals or HA from different aqueous media.