Heat moisture treatment (HMT) can be a useful method of wheat flour functionality modification, improving the nutritional value of pasta along with grape peels (GPF) addition. The aim of this study was to investigate the combined effects of HMT temperature, time, and moisture and GPF level on dough and pasta properties. Dough rheology and texture, pasta color, texture, total polyphenols (TPC), dietary fiber (DF), and resistant starch (RS) contents were evaluated. Furthermore, an optimization was performed based on Response Surface Methodology (RSM) and desirability function. The results showed that HMT regime and GPF determined proportional dough viscoelastic moduli and firmness increase. On the other hand, cooked pasta firmness and gumminess decreased with HMT conditions and GPF level rise. Higher pasta RS and DF content was promoted by HMT and GPF components. The reduction effect of HMT on TPC was countered by the incorporation of GPF, a rich source of polyphenols. The optimization revealed that the recommended wheat flour treatment regime would be 87.56 °C, 3 h, and 26.01% moisture, while the quantity of GPF that could be added was 4.81%. For these values, the maximum functional and nutritional values would be achieved with minimum negative impact on pasta quality.