Poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBH) is a bio-based polyester with the potential to replace some common polymers of fossil origin. However, PHBH presents serious limitations, such as low stiffness, tendency to undergo crystallization over long time periods and low resistance to thermal degradation during processing. In this work, we studied the use of alumina nanowires to generate PHBH-alumina nanocomposites, modifying the properties of PHBH to improve its usability. Solvent casting and melt blending were used to produce the nanocomposites. Then, their physicochemical properties and aquatic toxicity were measured. Finally, LCA was used to evaluate and compare the environmental impacts of several scenarios relevant to the processing and end of life (EoL) conditions of PHBHs. It was observed that, at low concentrations (3 wt.%), the alumina nanowires have a small positive impact on the stiffness and thermal degradation for the samples. However, for higher concentrations, the observed effects differed for each of the applied processing techniques (solvent casting or melt blending). The toxicity measurements showed that PHBH alone and in combination with alumina nanowires (10 wt.%) did not produce any impact on the survival of brine shrimp larvae after 24 and 48 h of exposure. The 18 impact categories evaluated by LCA allowed defining the most environmentally friendly conditions for the processing and EoL of PHBHs, and comparing the PHBH-related impacts to those of some of the most common fossil-based plastics. It was concluded that the preferable processing technique for PHBH is melt blending and that PHBH is unquestionably more environmentally friendly than every other analyzed plastic.