The effect of pasta-making processes on starch and protein features, as well as cooking behavior, and nutritional properties (i.e., resistant starch and starch in vitro digestibility) were assessed. Pasta from raw red lentils (R) was prepared by conventional extrusion (C_R) and extrusion-cooking (EC_R), whereas heat-treated red lentils (HT) were processed into pasta by conventional extrusion (C_HT). A “high protein” and “high fiber” pasta was prepared. Using HT was effective in increasing the luminosity (that was about 88, 91, and 96 for EC_R, C_R, and C_HT, respectively), and decreasing the presence of defects on the pasta surface (heterogeneity was 5%, 36%, and 45% for C_HT, EC_R, and C_R, respectively). Heat treatment on grains or flour significantly increased starch susceptibility to α-amylase (6.6, 7.4, and 8.6% for C_R, C_HT, and EC_R, respectively) and decreased the final viscosity (from 335 BU in C_R to 287 and 291 BU in EC_R and C_HT), resulting in a significant increase in starch digestibility (slowly digestible starch was about 41, 27, and 26% in C_R, C_HT, and EC_R, respectively). As regards proteins, the main effect on their structure was observed in C_HT, where the cooking behavior was much improved and cooking losses were lowest (5.7%). On the other hand, protein and starch organization in EC_R might have accounted for pasta resistance in overcooking.