Magnetic nanoparticles (MNPs) named Fe3O4@coPANI-PTH were synthesized by coating Fe3O4 nanoparticles (NPs) with a polyaniline (PANI)/polythiophene (PTH) co-polymer. The feasibility of Fe3O4@coPANI-PTH as the nanosorbent for magnetic solid-phase extraction (MSPE) was evaluated for the determination of Co(II) in real samples using microsample injection system – flame atomic absorption spectrometry (MIS-FAAS). Parameters (sample pH, adsorbent mass, eluent volume, sample volume, and co-existing ion effects) influencing the preconcentration of cobalt were optimized. Under the optimum conditions at pH 10, cobalt was completely adsorbed by 100 mg Fe3O4@coPANI-PTH from 60 mL sample and eluted quantitatively (≥ 95%) using 1.0 mL of 0.2% thiourea solution in a mixture of 2 mol L−1 HCl and 1 mol L−1 HNO3. The adsorption capacity and characteristics of Fe3O4@coPANI-PTH for cobalt were evaluated with isotherm studies. The accuracy of the optimized method was evaluated by measuring certified reference materials (CRMs) and spiked real samples. The relative error and standard deviation were below 6.0% for the CRM and real sample analyses. The limit of detection was 1.6 μg L−1. The determination of ultra-trace cobalt amounts in various soft drinks, spice, vegetable, and water samples was achieved satisfactorily with this method.