This work reports on the characterization of nanocomposites fully synthesized by bacteria, consisting ofpolyhydroxybutyrate-co-hydroxyvalerate (PHBV) matrices reinforced with bacterial cellulose nanowhiskers (BCNW). Two PHBV grades,with 9% HV (PHBV9) and 16% HV (PHBV16), were synthesized using food industry waste feedstocks and compared with a 3% HVcommercial grade (PHBV3). Whereas PHBV3 presented a high barrier performance but excessive brittleness, PHBV9 and PHBV16showed a more ductile behavior and reduced barrier properties. Subsequently, BCNW were incorporated into the PHBVs by a high-throughput electrospinning technique to produce master-batch formulations with relatively high nanofiller concentrations. The hybridultrathin fibers showed homogeneous morphologies and greater thermal stability than the pure PHBV fibers. Nanocomposites were thenproduced by melt mixing PHBVs with the hybrid fibers. Despite the low compatibility between the extremely hydrophilic BCNW andthe hydrophobic PHBVs, the nanofiller was highly dispersed and provided a reduction in oxygen permeability of the PHBV3 matrixwithout relevant modifications in mechanical performance.