Germination is a convenient technique that could be used to enhance the nutritional profile of legumes. Furthermore, consumers’ increasing demand for diversification of bakery products represents an opportunity to use such germinated flours in wheat-based products. Thus, this study aimed to underline the effects of soybean germinated flour (SGF) and lentil germinated flour (LGF) on the rheological behavior of dough during different processing stages and to optimize the addition level. For this purpose, flour falling number, dough properties during mixing, extension, fermentation, and dynamic rheological characteristics were evaluated. Response surface methodology (RSM) was used for the optimization of SGF and LGF addition levels in wheat flour, optimal and control samples microstructures being also investigated through epifluorescence light microscopy (EFLM). The results revealed that increased SGF and LGF addition levels led to curve configuration ratio, visco-elastic moduli, and maximum gelatinization temperature rises, while the falling number, water absorption, dough extensibility, and baking strength decreased. The interaction between SGF and LGF significantly influenced (p < 0.05) the falling number, dough consistency after 450 s, baking strength, curve configuration ratio, viscous modulus, and maximum gelatinization temperature. The optimal sample was found to contain 5.60% SGF and 3.62% LGF added in wheat flour, with a significantly lower falling number, water absorption, tolerance to kneading, dough consistency, extensibility, and initial gelatinization temperature being observed, while dough tenacity, the maximum height of gaseous production, total CO2 volume production, the volume of the gas retained in the dough at the end of the test, visco-elastic moduli and maximum gelatinization temperatures were higher compared to the control. These results underlined the effects of SGF and LGF on wheat dough rheological properties and could be helpful for novel bakery products development.