This study proposes a combination of optical and thermal methods to investigate the structural integrity of two 16th–17th centuries wooden panel paintings at the early stages of restoration. Well-established techniques, such as 3D scanning, technical photography, and active thermography, are combined with the less conventional shearography, which has recently gained increasing relevance in the diagnostics of cultural heritage materials. The proposed methodology enables the identification and spatial localization of different forms of degradation within the multilayered structure of the artworks, including physical-structural alterations, insect damage, localized hygroscopic degradation, nails, interlayer deterioration, and craquelure. This approach provides a comprehensive insight into the state of the panel painting structure and highlights potentially critical areas which were undetectable by visual inspection alone, demonstrating the ability to guide restoration interventions.