FDM (Fused Deposition Modeling) is one of the most used and industrially applied additive manufacturing processes due to its fast prototyping and manufacturing, simplicity, and low cost of the equipment. However, the mechanical properties of the printed products have a large dependence on orientation and interface strength between layers which is mainly related to the thermal union obtained. This thermal union has a large dependence on the melting and cooling down process. Additionally, the materials used must be extruded in a continuous filament before their use, which limits the materials used. However, a pellet extruder could be used directly in the printing equipment, avoiding filament extrusion. In this work, specimens of PLA (Poly(lactic acid)) with different bead orientations have been produced via filament or pellet extrusion to compare the effect of the different melting processes in the manufacturing methodology. Pellet extruded specimens showed higher infill and mechanical properties. These results were related to better adhesion between layers due to the longer melting and cooling process. The result was confirmed using DSC and XRD techniques, where a higher crystallinity was observed. A bicomponent specimen (50% pellet–50% filament) was prepared and tested, showing higher mechanical results than expected, which was, again, due to the better thermal union obtained in the pellet extruder.