Nano-biocomposites based on a biodegradable bacterial copolyester, poly(hydroxybutyrate-co-hydroxyvalerate), have been elaborated with an organo-modified montmorillonite (OMMT) clay as nanofiller, and acetyl tributyl citrate as plasticizer. The corresponding (nano)structures, thermal and mechanical properties, permeability, and biodegradability have been determined. Polyhydroxyalkanoates are very thermal sensitive then to follow the degradation the corresponding matrices have been analyzed by size exclusion chromatography. The results indicate that the addition of the plasticizer decreases the thermo-mechanical degradation, during the extrusion. These nano-biocomposites show an intercalated/exfoliated structure with good mechanical and barrier properties, and an appropriated biodegradation kinetic. Intending to understand the changes in the thermal properties, the nano-biocomposites were characterized by thermal gravimetric analysis and differential scanning calorimetry. The presence of the OMMT clay did not influence significantly the transition temperatures. However, the filler not only acted as a nucleating agent which enhanced the crystallization, but also as a thermal barrier, improving the thermal stability of the biopolymer. The results indicated that the addition of the plasticizer reduces the glass transition temperature and the crystalline melting temperature. The plasticizer acts as a processing aid and increases the processing temperature range (lower melting temperature).