For some applications of bioplastics like food packaging or medical devices, applying additives can be necessary to avoid microbial activity and hinder biofilm or fouling formation. A currently promising additive is chitosan (CS), the deacetylated form of the biogenic scaffolding material chitin. Due to its hydrophilicity, chitosan is not compatible with most of the thermoplastic bio-based polymers like poly(lactic acid) (PLA) or polyhydroxyalkanoates (PHA). In this work, compatibilization between chitosan and two selected bio-based polyesters, PLA and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), was enhanced by grafting maleic anhydride (MAH) and glycidyl methacrylate (GMA), respectively, onto polymer chains using peroxide. The success of grafting was confirmed via titration methods. The effects of grafting agent and peroxide concentrations on grafting reaction and the physical and thermal properties of the functionalized polyesters were investigated. Compounding of the functionalized polyesters with different weight portions of chitosan was accomplished in a discontinuous internal mixer by in-situ functionalization, followed by blending with chitosan. The titration method, scanning electron microscopy, DSC, FTIR and mechanical characterization of the composites showed good interfacial adhesion and suggest the formation of covalent bonds between functional groups of the polyesters and chitosan, especially for the samples functionalized with GMA. The molecular weights (Mw) of the samples showed a change in the molecular weight related to the thermal degradation of the sample. The Mw of the samples grafted with MAH are lower than those functionalized with GMA. Furthermore, integration of chitosan into non-functionalized PLA polymer matrix showed a nucleating effect, while for PHBV, the increase of crystallinity with the content of chitosan was only observed for grafted PHBV.