The electrospun nanosystems containing poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) and 1 wt% Fe doped ZnO nanoparticles (NPs) (with the content of dopant in the range of 0–1 wt% Fe) deposited onto polylactic acid (PLA) film were prepared for food packaging application. They were investigated by scanning electron microscopy (SEM), energy dispersive X-ray (EDX), Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), antimicrobial analysis, and X-ray photoelectron spectrometry (XPS) techniques. Migration studies conducted in acetic acid 3% (wt/wt) and ethanol 10% (v/v) food simulants as well as by the use of treated ashes with 3% HNO₃ solution reveal that the migration of Zn and Fe falls into the specific limits imposed by the legislation in force. Results indicated that the PLA/PHBV/ZnO:Fex electrospun nanosystems exhibit excellent antibacterial activity against the Pseudomonas aeruginosa (ATCC-27853) due to the generation of a larger amount of perhydroxyl (˙OOH) radicals as assessed using electron paramagnetic resonance (EPR) spectroscopy coupled with a spin trapping method.