Discontinuous fibre reinforced composites enable the manufacture of integrated structural components via the complex flow process of compression moulding. However, such processes can lead to the formation of detrimental weld-lines. Here, the meso-structure of carbon fibre sheet moulding compounds (C-SMC) was analysed using conventional non-destructive techniques and automated eddy current (EC) scanning, as well as destructive methods, in an attempt to identify defects such as weld-lines in this class of materials. Compression-moulded plaques with forced weld-lines in two different configurations (adjacent and opposing flow joints) were analysed, showing up to 80% strength reduction versus a defect-free plaque. The EC-determined local fibre orientation and elucidated local microstructure matched those obtained using conventional techniques, showing a dramatic fibre tow alignment parallel to the weld-lines. It was found that failure occurred in proximity to the “non-uniformity” defect regions identified by EC analyses, demonstrating the use of robot-guided EC for successful defect detection in C-SMC structures.