Controlled germination is recognized for its potential to enhance both the nutritional profile and functional properties of grains, but there is limited information about the level of wheat germination that promotes functional changes without losing breadmaking potential. This research aims to analyze the physicochemical changes in wheat during germination for 36 h, focusing on evaluating kernel changes, the flour breadmaking functionality, and bread characteristics. Pasting properties progressively decreased as the germination progressed, and apparent viscosity was barely detected after 36 h germination. Initial decline in gluten index was observed at 24 and 36 h germination, but gluten kept its aggregation capabilities. Optimal germination periods of 6–18 h significantly improved flour functionality, evidenced by increased Gluten Performance Index, gluten index, and enhanced dough mixing properties. Further, mini-breads, developed after optimizing breadmaking conditions, displayed increased 2D areas in 24 and 36 h and lower crumb hardness in 24 and 36 h of germinated bread compared to those obtained with sound wheat flour. Significant correlations were found among alpha amylase activity, Falling number, total and damaged starch content, RVA parameters, gelatinization enthalpy, and breadcrumb texture parameters. Developing mini bread using different levels of germinated flour demonstrates its viability for breadmaking offering a promising innovation within the whole-grain food industry.