Natural fibers constitute an interesting alternative to synthetic fibers, e.g. glass and carbon, for the production of composites due to their environmental and economic advantages. The strength of natural fiber composites is on average lower compared to their synthetic counterparts. Nevertheless, natural fibers such as flax, among other bast fibers (jute, kenaf, ramie and hemp), are serious candidates for seismic retrofitting applications given that their mechanical properties are more suitable for dynamic loads. Strengthening of structures is performed by impregnating flax fiber reinforced polymers (FFRP) fabrics with epoxy resin and applying them to the component of interest, increasing in this way the load and deformation capacities of the building, while preserving its stiffness and dynamic properties. The reinforced areas are however prompt to debonding if the fabrics are not mounted properly. Nondestructive testing is therefore required to verify that the fabric is uniformly installed and that there are no air gaps or foreign materials that could instigate debonding. In this work, the use of active infrared thermography was investigated for the assessment of (1) a laboratory specimen reinforced with FFRP and containing several artificial defects; and (2) an actual FFRP retrofitted masonry wall in the Faculty of Engineering of the University of L’Aquila (Italy) that was seriously affected by the 2009 earthquake. Thermographic data was processed by advanced signal processing techniques, and post-processed by computing the watershed lines to locate suspected areas. Results coming from the academic specimen were compared to digital speckle photography and holographic interferometry images.