The extraordinary growing demand for environmentally friendly materials leads to an increasing attention on the use of biopolymers. The Poly-lactid acid is one of the most promising biopolymers, with very interesting physical and mechanical properties. However, the low rate of crystallization of the PLA compared to other semi-crystalline polymers limits its use in technical applications. In this study, the effect of the application of a system able to rapidly change the temperature of the cavity surface on the final crystallinity of Poly-lactid acid micro-parts was studied. The technique adopted is based on the use of very thin heating elements, thermocouples and insulation layers that can be attached near the surface of the cavity allowing a precise and local control of the temperature during each stage of the molding cycle. The system was adopted to increase the temperature of the cavity up to 160 °C during the filling stage to permit the filling of a cavity with a thickness of 0.2 mm and an aspect ratio equal to 50. After the filling, the system allowed the application of rapid temperature variations locally along the sample. Different thermal histories were applied to tune the morphology of the parts. Calorimetric analyses permitted to understand the crystallization behavior of the processed material and determine the final crystallinity in the produced samples.