The nutritional benefits of Lentil (Lens culinaris Medik.) have been widely acknowledged. Enriching wheat flour using pulses such as lentil flour is a way of increasing both the nutritional and functional content of wheat-based foods. The properties of lentil that may have specific health benefits to the individual are also widely acknowledged. Functional compounds from plant-based foods are commonly attributed to polyphenols, inhibitors, vitamins, and soluble and insoluble fiber. Water-soluble carbohydrates, (WSCs) consisting predominantly of oligosaccharides, make up part of total dietary fiber. The beneficial role of oligosaccharides promoting probiotic health is widely acknowledged. Equally, it is recognized that oligosaccharides cause irritable bowel syndrome limiting the ability for some individuals in consuming pulses. Findings: We investigated changes in water-soluble carbohydrate (WSC) composition during the dough fermentation phase of bread making and quantified the residual WSC in the bread. As expected, the addition of lentil flour increased the WSC profile of the resulting composite flours which included raffinose, stachyose, ciceritol, and verbascose. A threefold decrease was observed only for verbascose during the dough mixing phase; however, during fermentation, raffinose and stachyose decreased, but ciceritol was not affected. Conclusions: The baking process may reduce the effects of IBS suffered by some individuals who consume lentil products prepared by traditional methods. Our study concluded that bread prepared from wheat–lentil flour results in a more complex carbohydrate profile and may potentially enhance the prebiotic functionality compared with bread made from wheat alone. Significance and novelty: It is now recognized that alternate sources of protein can be gained using plant-based constituents. The functional properties of plant-based compounds are also widely accepted. Processing, such as fermentation and baking, can alter the concentration and functionality of plant-based compounds. In this study, we identified the changes in carbohydrate composition that occur in a wheat–lentil composite flour under the conditions of fermentation and baking.