Plant protein-based fibrous structures have recently attracted attention because of their potential as meat replacer formulations. It is, however, unclear how the process conditions and fortification with micronutrients may affect the chemical stability of such products. Therefore, we aimed to investigate the effects of process conditions and the incorporation of iron (free and encapsulated) on protein oxidation in a soy protein-based fibrous product. First, the physicochemical stability of iron-loaded pea protein particles, used as encapsulation systems, was investigated when exposed to 100 or 140 °C. Second, protein oxidation was measured in the iron-fortified soy protein-based fibrous structures made at 100 or 140 °C. Exposure to high temperatures increased the carbonyl content in pea protein particles. The incorporation of iron (free or encapsulated) did not affect carbonyl content in the fibrous product, but the process conditions for making such products induced the formation of carbonyls to a fairly high extent.