Barium ferrite encapsulated polythiophene (BaFe12O19/PTh) nanocomposite has been synthesized to analyse electromagnetic interference (EMI) shielding. The morphological analysis of the synthesized composites has been investigated by scanning electron microscopy (SEM), which confirmed the encapsulation of BaFe12O19 nanoparticles by PTh forming a core-shell structure. Highest loading of BaFe12O19 in composite (NC-100 i.e. BaFe12O19:PTh = 1:1) exhibits excellent magnetic properties with a magnetic moment and coercivity of 25.78 emu/gm and 2.5 kOe, respectively. Microwave shielding behaviour of the nanocomposite samples has been tested in X-band region by vector network analyser. Highest −43.27 dB shielding effectiveness at 11.65 GHz has been obtained in NC-100 composite. The excellent shielding effectiveness is due to the synergistic effect of dielectric and magnetic loss of the nanocomposite. These results suggest that the BaFe12O19/PTh nanocomposite (NC-100) exhibited superior EMI shielding properties and find wider application as low cost, high performance, lightweight microwave absorbing material. Display omitted •Synthesis of BaFe12O19/PTh nanocomposite by in-situ emulsion polymerization.•The nanocomposite exhibits excellent magnetic and thermal properties.•EMI shielding properties the nanocomposite has been investigated in the X-band.•Maximum shielding effectiveness of −43.27 dB at 11.65 GHz has been obtained.