Polyhydroxyalkanoates (PHAs) are polyesters that can be produced from industrial wastewater or surplus products by mixed microbial cultures (MMC). To optimise PHA production by MMCs, the link between the microbial structure and function of these enrichments must be better established. This study investigates, for the first time, the impact of operational changes on the microbial community and the associated process performance of PHA producing MMCs. It was found that a PHA producing community fed with fermented molasses was dominated by a combination of Azoarcus, Thauera and Paracoccus, where the former two groups were present in highest abundance. Dominance of either Thauera or Azoarcus seemed to be determined by the organic loading rate imposed in the selection reactor. While higher Azoarcus enrichments led to higher PHA production yields and lower biomass growth yields as compared to Thauera, the Thauera abundance was strongly linked to higher hydroxyvalerate (HV) fractions. Paracoccus abundance was correlated with a lower PHA production capacity as compared to Azoarcus, and produced lower HV fractions than Thauera and Azoarcus. The findings of this study suggest that MMCs targeting the enrichment of Azoarcus as the primary biomass fraction with Thauera as a minor fraction lead to optimal specific PHA production and polymers with high HV content, which is likely to improve their mechanical properties.