The solvent mixing process is a utile production technique to promote the cost-effective preparation of lightweight and flexible electromagnetic interference (EMI) shield films based on binary polymer-based conductive nanocomposite material with a very low electrical percolation threshold. Here in, a facile preparation of conductive binary biodegradable polymer nanocomposite films comprised of ester-based thermoplastic polyurethane (TPU), and poly (butylene adipate -co-terephthalate) (PBAT) is reported where the acid-functionalized multiwalled carbon nanotube (MO) has been preferentially incorporated into the PBAT phase of the binary polymer matrix and to get effective nanofiller dispersion we employed solvent mixing technique. For the effective reduction of “e-wastes” biodegradability is new generation demand for polymer nanocomposites. The PBAT/TPU based biodegradable binary blend has not been used before to fabricate polymer nanocomposite material. The 0.8 mm thick polymer nanocomposite film with the loading of around 5 wt% of MO is considered as the nanocomposite film achieving the electrical percolation threshold indicated by a sudden jump in the total EMI shielding effectiveness (EMI SE) value from − 17 to − 24 dB (within the frequency region from 8.2to 12.4 GHz) if the MO content is upgraded from 3 to 5 wt%. A loading of 10 wt% of MO gives − 30 dB of EMI SE at 8.2 GHz. The preferential distribution of MO filler in the PBAT phase has been confirmed by FTIR, DMA, selective dissolution test, HRTEM, and FESEM characterization techniques.