Roasting is an important step in cocoa processing causing water loss and generating volatile compounds responsible for chocolate aroma like nitrogen-heterocycles. In this study, the comparison of two techniques, oven roasting, and fluidized bed roasting, in terms of effective water diffusivity (De) and activation energies of formation (Ea) of nitrogen-heterocycles was achieved with cocoa nibs. Fluidized bed roasting, recognized for its energy efficiency and low-footprint synthesis, was 16 times faster than oven roasting. The order of magnitude of De in fluidized-bed-roasted nibs was −8, while it was −9 in the oven-roasted nibs. Moreover, the aw was 50% higher in fluidized-bed-roasted nibs than in the oven-roasted ones. The Ea of nitrogen-heterocycles ranged roughly between 40 and 80 kJ/mol. Those values were lower under fluidized bed roasting than under oven roasting. The more effortless water mobility within fluidized-bed-roasted cocoa demanded lower Ea, and favored the formation of nitrogen-heterocyclics. Industrial relevance: This study can inspire cocoa manufacturers and equipment designers to pursue the formation of nitrogen-heterocycles during the roasting process of cocoa. It can be done either by adapting and scaling the current fluidized bed coffee roasters to cocoa beans or nibs; or by exploring other alternatives capable of leading enough water diffusivity and water activity in the cocoa nibs, as reported here. These physicochemical conditions undoubtedly boosted the formation of volatile compounds responsible for chocolate aroma, e.g., the pyrazines, without carrying the formation of typical-burn volatile compounds. This natural way of favoring the generation of pyrazines in cocoa nibs could contribute to clean labels by reducing or avoiding the subsequent use of flavorings. The implementation of efficient heat-transfer techniques during roasting, e.g., fluidized bed roasting, could reduce the processing cost and improve sustainability. Studies in the matter of sensory profile, and energy consumption/conversion are called for future research.