This study investigates the microstructure and compressive behaviour of PLA/PHA-wood lattice structures manufactured using fused filament fabrication (FFF). The primary objective is to evaluate the effects of defects, such as porosity and surface roughness, on the mechanical properties of these lattice structures. X-ray micro-tomography (XRT) and finite element analysis are employed to compare CAD models with real lattice structures, offering insights into defect-induced performance deviations. The novel approach integrates experimental and numerical methods to better understand damage accumulation in porous structures. The methodology includes uniaxial compression testing and image processing for microstructural characterization. Results reveal significant differences in relative density and stress concentration due to manufacturing defects. In particular, 3D printed lattice structures display typical cellular material behaviour with a primary bending deformation mechanism. X-ray tomography reveals that process-induced porosity generate stress heterogeneity, which is not captured from CAD-based model resulting in an overestimation of the stiffness. The study concludes that accounting for these defects can be quantified by shifting the target relative density to compensate lack of performance in 3D-printed lattice materials.