This study investigated the design of a tray bioreactor for solid-state fermentation, applying Rhizopus oryzae to oilseed meals as the substrate. Two process variables were continuously monitored in the bioreactor to ensure precise control of the environmental conditions: temperature and relative humidity (RH). The comprehensive analysis covered the effects of different fermentation conditions on the protein content, technological properties, and molecular distribution of the samples. The study revealed that the configuration factors suffered a stratification within the three trays of the bioreactor. Notably, the upper tray registered the largest dispersion, with a range of 1.5 °C. When analyzing the differences between sensors within each tray, the largest difference was found in the lower tray (10.9%). Furthermore, higher EAI (Emulsifying Activity Index) values were observed in the upper tray (T3) for rapeseed. As for ESI (Emulsion Stability Index) values, no differences were observed between the trays or fermentation periods. Using the changes induced by Rhizopus oryzae fungal enzymes, the study quantitatively examined the changes in the by-product valorization. While the bioreactor factors did not affect the protein quantity itself, they had significant impacts on specific changes within the molecular weight protein fraction. The findings of this study offer significant insights into the complex dynamics of solid-state fermentation processes. The outcomes of this study not only advance understanding of solid-state fermentation but also offer practical guidance for the design and operation of fermenters in industrial applications.