Considerable amounts of agro-industrial by-products are discarded or burnt as fuel every year. However, they can be utilized as a valuable source of fiber, phenolics and other useful compounds such as antioxidants. The profile of beneficial compounds can be affected by genotype, locality, orchard management and productive season, adding or decreasing the bioactive potential of by-products. In this study, hazelnut (Corylus avellana L.) and walnut (Juglans regia L.) nutshells were investigated for their fiber content and antioxidant capacity as valorized by-products for the industry. Determinations (ORAC, TPC and color asses) were performed in hazelnut and walnut orchards located in Southern Chile during three consecutive seasons (2020/21; 2021/22 and 2022/23). Analyses of oxygen radical absorbance capacity (ORAC) in nutshells showed the highest ORAC from both species in the season 2020/21 (3217 µmol TE g1DW for hazelnut shells and 4663 µmol TE g DW1 for walnut shells), while variability in the consecutive seasons was lower for hazelnut than in walnut. Total phenolic content in hazelnut shells was positively correlated with L* (R: 0.883) and E (R: 0.924) during 2020/21 season, also with L* for 2022/23 (R: 0.907). While ORAC was negatively correlated with L* (R: 0.922) in 2021/22. In addition, morphological and structural features of both nutshells examined by Scavenging Electron Microscopy (VP-SEM) and Confocal Scavenging Laser Microscopy (CSLM) revealed differential tissue distribution and accumulation patterns of both cellulose and lignin. On the other hand, photo-colorimetric values were determined for both shells and corresponding seasons, and non-significative differences were found both shells and among seasons Finally, these results provide insight into the physicochemical characteristics of two shell types which should be considered together with antioxidant capacity in their valorization as a residual material.