The goal of this study was to investigate the effect of extrusion-forced structural changes on the extent of functional and biochemical changes of three selected protein sources that are predominantly used in aquafeed, i.e., fish meal (FM), soybean meal (SBM), and distillers dried grains with solubles (DDGS). The samples were individually extruded in a single-screw extruder using a factorial design with replicated central composite points at a temperature of 80, 110, and 140°C; screw speed of 80, 150, and 220 rpm; and moisture content of 150, 225, and 300 (g/kg). Extrusion temperature and feed moisture significantly affected the nitrogen solubility in water (NSI), sodium dodecyl sulfate, and 2-mercaptoethanol solvents. Screw speed had only a minor effect on this value (P < 0.05). Solubility results indicated that the contribution of hydrophobic and ionic interactions were more significant than that of the disulfide bonds, particularly for FM and SBM extrudates. For all extrudates, the highest peak viscosity was observed at the highest temperature and lowest screw speed. Extrusion processing led to considerable increase in T g of 79 % and 67 % for the DDGS and SBM samples, and a reduction of 19 % for the FM sample, respectively. Extrusion processing increased relative protein digestibility (RPD) of the SBM extrudates the most, followed by those of DDGS and FM. Overall, the severity of the extrusion conditions adversely affected available lysine content (AL) and L* color score, but relatively increased RPD of the extrudates. SBM extrudates had the lowest reduction in AL. Despite the decrease in AL, the results for both plant-based protein extrudates were comparable in quality to those of FM. The outputs of this study provide viable information for feed formulator and feed technologist in feed and food industries.