A study of controlling the microwave mitigation properties of ferrite-carbon black/PVA composites by tuning the magnetic microstructure and spin arrangement of the ferrite particles is presented. MxCo(1-x)Fe2O4 (M: Ni2+, Mn2+ & Zn2+) nano-ferrites (NFs) were synthesized by a solvothermal method and these NFs were used to fabricate NF-CB hybrids and flexible NF-CB/PVA composite films. The magnetic force microscopy studies of the NFs reveal a unique single axis oriented domain structure for Zn-NFs and multi-domain magnetic microstructures for Mn-NFs and Ni-NFs. Mössbauer analysis of the NFs reveals highly distorted co-ordination of Fe3+ cations in Zn-NFs, whereas sub-lattice spins are canted in Mn-NFs and Ni-NFs. Despite the distorted magnetic lattice and broken coordination, the largest microwave shielding effectiveness (SE) of 32 dB is observed, over a bandwidth of 8 to 18 GHz, for Zn-NF-CB/PVA with a major contribution from absorption (SEA∼ 25 dB). The dielectric properties and Cole-Cole plots indicate enhanced interfacial polarization in Zn-NF-CB/PVA, which is attributed to the motion of polarons across multiple heterogeneous interfaces. These polarons are thought to be generated by distorted co-ordination of Fe3+, and d-d electron transition between Co2+⇋ Fe3+ cations at the B-site of Zn-NF. Distorted co-ordination of Fe3+ in Zn-NF along with unique single axis oriented magnetic domains play a crucial role in magnetic losses, as μ'' is almost double in Zn-NF based composites as compared to other composites. Due to their excellent and tunable microwave absorption properties, NF-CB/PVA composites could be employed for next generation stealth applications.