Chocolate is a widely consumed product with high levels of polyphenols; unfortunately, it is reduced during the process. Adding other components allows for counteracting the polyphenols lost during chocolate processing and reducing the content of unsaturated fatty acids, affecting its physical properties. This study identified the conching time, concentration of sauco by-products, and levels of sacha inchi oil to produce enriched dark chocolates. For this study, sauco by-products in percentages of 2, 6 and 10%, sacha inchi oil in levels of 1, 3, and 5%, and three conching times of 16, 20, and 24 h were added to 75% dark chocolates, and the process conditions were optimized through the response surface methodology (RSM). The physicochemical properties of the dark chocolates were studied, observing that the sauco by-product, sacha inchi oil, and conching time significantly affected (p < 0.05) the variables of antioxidant activity, total phenol content, rheology, hardness, and particle size. The R correlation of the factors declared against the variables indicated the model's reliability as it was close to 1. The results suggest that incorporating sauco by-products allows for obtaining chocolates with good chemical properties; however, high percentages of sacha inchi oil and shorter conching time cause a negative effect on the chocolate affecting the physical properties.