Processed wheat bran (W) is of great importance for food and feed. Consequently, the biosafety of W should be evaluated and improved with valorisation strategies. This study tested a design combining extrusion (at temperature of 115 and 130 °C; screw speeds of 16, 20, and 25 rpm) and fermentation with Lactobacillus plantarum and L. uvarum strains for the valorisation of W to provide safer food and feed stock. The influence of different treatments on biogenic amine formation, mycotoxin content, and free amino acids, as well as acidity, microbiological parameters, and sugar concentration, were analysed. This research showed that a combination of extrusion and fermentation with selected strains can change several aspects of W characteristics. There was a significant effect of applied treatments on acidity and the microbiological parameters of W, as well as biogenic amines content. The lowest total mycotoxin concentration (29.8 µg/kg) was found in extruded (130 °C; 25 rpm) and fermented with L. uvarum sample. Finally, the combination of the abovementioned treatments can be confirmed as a prospective innovative pre-treatment for W, capable of potentially enhancing their safety characteristics and composition.