Radar-absorbing materials (RAMs) are classified as a vital material sector in stealth technology and electromagnetic interference (EMI) shielding. This work introduces Ni-Cu-Al ferrite/polypyrrole (PPy) nanocomposites synthesized using citrate precursor auto-combustion technique combined with an in-situ polymerization method. This interface engineering approach significantly improves homogeneity, interfacial interactions, and the synergistic electromagnetic properties of the prepared nanocomposites. Detailed characterization has been conducted on Ni0.5Cu0.5AlxFe2-xO4 (x = 0.0, 0.2, 0.4) nano-ferrites and their composites with PPy. The formation of a single-phase cubic spinel structure was confirmed by X-ray diffraction (XRD); the lattice constants decreased upon aluminum (Al) substitution, which was attributed to the reduced ionic radius magnitude of Al. Additionally, the successful coating of PPy and the integrity of the spinel structure were confirmed by Fourier transform infrared (FTIR) spectra. Moreover, scanning and transmission electron microscopy analyses showed homogeneous particle distributions with increased agglomeration and decreased crystallite sizes due to the addition of PPy. Furthermore, vibrating sample magnetometry (VSM) analyses demonstrated a significant reduction in saturation magnetization. This is due to Al substitution and the PPy coating, which are considered non-magnetic and consequently lead to a decline in magnetic parameters. The electromagnetic characterization using a vector network analyzer (VNA) showed that PPy-coated Ni-Cu-Al ferrite presented enhanced dielectric and magnetic losses and, hence, higher total shielding effectiveness (SET) of up to 27 dB in the 2–18 GHz frequency range. Optimized impedance matching with high attenuation constants was observed for Ni0.5Cu0.5AlxFe2-xO4/PPy nanocomposite for x = 0.2 due to the synergistic dielectric-magnetic losses, interfacial polarization, and conductive network formation. These results reveal the potential of Ni0.5Cu0.5AlxFe2-xO4/PPy nanocomposites, especially the moderately Al-substituted materials, for applications involving advanced EMI shielding and stealth.