The thermal stability of poly(3-hydroxybutyrate) (PHB) in an oxidation environment was investigated in bulk at temperatures ranging from 100 °C to 140 °C. The process carried out in pure oxygen resulted in PHB backbone degradation with resulting non-volatile products typical for regular PHB thermal degradation while thermal treatment of PHB in an oxygen/ozone mixture resulted in increased rate of polymer backbone scission. The non-volatile degradation product contained macromolecules with several types of terminal groups but also a part of the 3-hydroxybutyrate repeating units was transformed into 3-malic acid units. NMR and multi-stage MS characterization revealed the random distribution of 3-malic acid units in the oligomeric products as well as the content of the malic acid units being dependent on oxidation conditions.