This work aims to evaluate the effect of the addition of a high-protein hydrolyzed (HPH) flour from the chemical silage of trout (Oncorhynchus mykiss) residues on the parameters of the extrusion system physicochemical transformations and the microstructure of the extrudate. During the extrusion process, the materials used for the study were the HPH flour obtained from trout by chemical silage, fishmeal, and cassava starch. The extrudate’s microstructural changes were evaluated by determining the porosity, scanning electron microscopy, the chemical changes, the amino acid profile, residual formic and lactic acid content, the molecular mass profile, the grade of hydrolysis, and in vitro digestibility. The results showed pellets with high durability due to the cohesiveness of the hydrolyzed protein flour but at the same time with low hardness due to the high porosity achieved. The monitoring carried out to the changes in the protein, such as the degree of hydrolysis, water-soluble protein, and molecular mass profile, verify the binding effect of the high-protein hydrolyzed flour during the extrusion process. Finally, the high-resolution optical microscopy methodology presented a high correlation with the phenomena presented in the experiment.