FeNi (iron-nickel) alloy particles were coated with MWNTs (Multiwalled carbon nanotubes) using simple ball milling technique at various alloy to MWNT ratios. These hybrid heterostructure were then dispersed in PVDF/TPU (Polyvinylidene fluoride/ Thermoplastic polyurethane) blends to develop flexible composite materials that can shield electromagnetic (EM) radiations. These alloy particles coated with MWNT localise mostly in the TPU phase of the binary blends. The shielding effectiveness (SE) measurements obtained from the scattering parameters reveal that for a particular ratio of FeNi/MWNT (3:1), the SE was the highest (-35.7 dB) among the different composites studied here and manifested in improved microwave absorption in the blends. The absorption driven shielding is due to various polarization in the shield, thereby increasing the dielectric loss. It was observed that these MWNT wrapped magnetic alloy particles shielded the incoming EM radiations more effectively as compared to only MWNTs or only alloy particles. The soft nanocomposites designed here absorb up to 95 % of the incoming EM radiations. The lowest skin depth and highest specific EMI (Electromagnetic interference) shielding attained was 1.4 mm and −20.5 dB cm2 g−1 respectively for composites containing FeNi/MWNT- 3:1. The attenuation constant derived from different parameters of these blends were also analysed in order to develop a multi-layered structure, having absorption-multiple reflection-absorption pathways. This was used to assess the effect of different layers and their sequence in the multi-layered structure on final EM wave attenuation. Interestingly, multi-layered architecture with a similar thickness showed three-fold increase in the total shielding as compared to their bulk counterpart. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim