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The utilization of food waste and sewage sludge as organic substrate from urban context for the synthesis of microbial polyhydroxyalkanoates (PHAs) has been only recently investigated at pilot scale. Within this context, two stabilization methods have been found for preserving the amount of PHA intracellularly produced by open mixed microbial culture (MMC): thermal drying and wet acidification of the biomass at the end of PHA accumulation process. The extracted PHA from the two differently stabilized biomasses was then characterized with regard to chemical composition, molecular weight, and thermal properties. The polymer contained two types of monomers, namely 3-hydroxybutyrate (3HB) and 3-hydroxyvalerate (3HV) at a relative percentage of 93.0–79.8 and 7.0–20.2 w/w, respectively. PHA extracted from wet-acidified biomass had higher average molecular weights (Mw) of 370–424 kDa while PHA recovered from thermally stabilized dried biomass had a 3-fold lower Mw (on average). The PHA decomposition temperatures Td10% and Tdmax were in the range 260–268 °C and 269–303 °C, respectively, not dependent on the monomeric composition or molecular weight. Thermal properties such as melting temperature (Tm1 132–150 °C; Tm2 155–167 °C) and melting enthalpy (26–70 J/g) were quantified in a relatively broad range according to the different stabilization-extraction method and obtained composition.