The aim of this study was to investigate the impact of two types of fish raw material on fishmeal (FM) physicochemical properties, specific mechanical energy, starch gelatinization and physical feed quality. Eleven feed mixes based on six independent FMs from herring (FMH) and five from sand eel (FMSE) were extruded according to standardized conditions. Type of fish raw material influenced FM physicochemical properties and had significant impact on starch gelatinization and pellet hardness. Multivariate models were established based on partial least squares regression (R2 = 0.637–0.999). Improved degree of starch gelatinization was associated with increased degree of protein hydrolysis (P = 0.011) and by replacement of FMH with FMSE in the feed mix (P = 0.012). A large span in pellet hardness was observed (4.9–94.1 N). Improved hardness was associated with decreased level of non-soluble protein (P < 0.001) and by replacement of FMSE with FMH (P < 0.001). For FMSE, improved hardness was associated with decreased level of non-soluble protein (P < 0.001) and increased degree of protein hydrolysis (P = 0.002), compressed bulk density (P = 0.039) and dust fraction (P = 0.001). The underlying physical and chemical mechanisms are discussed. The study documents differences in technical quality of FM produced from herring and sand eel with significant impact on fish feed extrusion and pellet quality.