The effect of modification of sisal fibre with propionic anhydride and vinyltrimethoxy silane on the microbiological stability of poly(hydroxybutyrate-co-valerate) (PHBV) was investigated. The effect of the coupling agent – PHBV grafted with maleic anhydride (PHBV-g-MA) was also investigated. The best adhesion at the interface was observed for propionylation of sisal fibre, which improved the thermal properties of the composites. Composites with modified sisal fibre were characterized by higher activation energy (155 kJ/mol), which is related to stronger interactions at the matrix-fibre interface. In the microbial growth test, all biocomposites showed a decrease in molecular weight due to enzymatic degradation by Aspergillus niger. The most resistant to microorganisms was the composite containing propionylated sisal fibre. DMTA and TGA also confirmed the highest microbiological stability of the composite with the addition of propionylated sisal fibre, as evidenced by the smallest change in the properties after the microbiological growth test. In contrast, PHBV-g-MA caused significant enzymatic degradation due to the presence of large amorphous regions.