The effect of process parameters on the final properties of a poly-lactic acid (PLA) and polyhydroxybutyrate (PHB) polymer blend filled with nanoclays was evaluated. To this aim, the nanofilled blend was processed in a co-rotating twin screw extruder, considering three different screw profiles and different values of the screw rotation speed, and the thermal and thermo-mechanical properties of the so-obtained materials were investigated. Furthermore, XRD analyses, SEM observations and rheological characterization were exploited to infer the coupled effect of the process parameters and nanoclay presence on the microstructure of the filled blend. Preliminary thermodynamic calculations allowed predicting the preferential localization of the nanoclay in the interfacial region between the polymeric phases. The relaxation mechanism of the particles of the dispersed phase in nanofilled blend processed, by rheological measurements, is not fully completed due to an interaction between polymer ad filler in the interfacial region with a consequent modification of the blend morphology and, specifically, a development of an enhanced microstructure. Therefore, by varying the screw configuration, particularly the presence of backflow and distribution elements in the screw profile, high shear stresses are induced during the processing able to allow a better interaction between polymers and clay. This finding also occurs in the thermo-mechanical properties of material, as an improvement of storage modulus up to 20% in filled blend processed with a specific screw profile. Otherwise, the microstructure of filled blend processed with different screw speed is similar, according to the other characterizations where no remarkable alterations of materials were detected.