This study investigated the impact of substituting wheat with pulse flours (lentil, chickpea, lupin, green and yellow pea) on reactivity during different steps of sponge cake development. Pulses exhibited a greater ability to generate volatiles with probable odor activity. Batter beating initiated lipid oxidation which depended on lipoxygenase activity and the fatty acid profile of the flours. Among the pulses, pea batters were richest in oxidation markers whereas lupin was least reactive, probably due to thermal pre-treatment. Baking triggered caramelization and Maillard reactions, notably with the pulse products which were particularly enriched in pyrazines and furanic compounds. Principle component analysis revealed that pea cakes were associated with oxidation markers that typically possess green-beany flavors, while Maillard markers known to impart nutty, roasted notes were assigned to lentil and chickpea cakes. These findings highlight the importance of ingredient type and its pre-processing in the development of quality-related markers for gluten-free products.