As they cannot massively accumulate in our eco-system, biodegradable polymers represent one of the solutions to mitigate plastic pollution. Meanwhile their ability to be recirculated before being biodegraded is important to maximize their economic value. Like all other polymers, their ability to be recycled and reused is highly dependant of their thermal stability, which also deserves to be investigated. Here, we clarify the potential impact of two natural phenolic additives, quercetin and gallic acid on the thermal stability of a promising microbial biodegradable polyester, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). The effect of the structure and the percentage of polyphenols (0 to 15 wt%) on the morphological behaviour and thermomechanical stability of PHBV was studied. Up to 5wt%, homogeneous blends characterized by intermolecular bonding interactions between the phenolic compounds and the polymer matrix were obtained. Above this percentage, a phase separation was observed in the presence of quercetin, while gallic acid crystals were embedded into the PHBV matrix, hindering its crystallization. It was concluded that regardless the additive percentage, the structural evolution of PHBV during the thermal treatment was strongly affected by the polyphenol structure: Quercetin slightly improved the structural integrity and thermo-mechanical stability of PHBV, while the carboxylic group of gallic acid contributed to auto-catalyse the polymer chain scission, accelerating its degradation.