Hierarchical functionalization of flax fibers with ZnO nanostructures was achieved by electroless deposition to improve the interfacial adhesion between the natural fibers and synthetic matrix in composite materials. The structural, morphological, thermal and wetting properties of the pristine and ZnO-coated flax fibers were investigated. Thus, the ZnO-coated flax fabric discloses an apparent contact angle of ~140° immediately after the placement of a water droplet on its surface. An assessment of the interfacial adhesion at the yarn scale was also carried out on the flax yarns coated with ZnO nanostructures. Thus, after the ZnO functionalization process, no significant degradation of the tensile properties of the flax yarns occurs. Furthermore, the single yarn fragmentation tests revealed a notable increase in the interfacial adhesion with an epoxy matrix, reductions of 36% and 9% in debonding and critical length values being measured compared to those of the pristine flax yarns, respectively. The analysis of the fracture morphology by scanning electron microscopy and X-ray microtomography highlighted the positive role of ZnO nanostructures in restraining debonding phenomena at the flax fibers/epoxy resin matrix interphase.