Thermoplastic composites with a PLA matrix are of commercial interest due to their bio-based nature and biodegradability. The main obstacle to their use in more demanding applications is their fragility and limited exploitation temperature. The present work describes the use of PLA in combination with polycarbonate (PC) and the addition of nanocrystalline cellulose (NCC) without prior surface treatment. Reactive compatibilizers were used in the production process to simultaneously produce a homogeneous thermoplastic mixture of PC and PLA and to enhance the surface interactions among NCC and the PC/PLA blend and additives. We performed a comparison between injection moulding and 3D printing using Fused Granule Fabrication (FGF) technology. The best results were obtained with the reinforcement of 1 wt% NCC in the PC/PLA matrix with compatibilizer and additives. Reactive extrusion with a thermoplastic mixture of PC and PLA reinforced with 1 wt% NCC with additives enhanced impact strength by more than 160% and toughness evaluated by tensile tests by more than 90% regarding to neat PLA in injection moulded parts. The comparison between injection-moulded and FGF parts showed that the stiffness was higher and the strength and toughness were lower in FGF parts than in injection-moulded parts.