Roasting cocoa beans by means of microwave radiations seems to be a potential alternative to convection roasting, but little is known about the impact of this method on the perceived flavor profile of the chocolate. Therefore, this research focused on revealing the flavor perception of chocolate produced with microwave roasted cocoa beans assessed by both a trained panel and chocolate consumers. Samples of 70% dark chocolate produced from cocoa beans microwave roasted at 600 W for 35 min were compared with samples of 70% dark chocolate produced from cocoa beans convectively roasted at 130 °C for 30 min. Non-significant differences (p > 0.05) in the measured physical properties, such as color, hardness, melting, and flow behavior, showed that chocolate produced from microwave roasted cocoa beans can exhibit the same physical qualities as convection roasted chocolate. Moreover, combined discriminative triangle tests, with 27 judgements in total, performed by a trained panel, showed that each type of chocolate exhibited distinctive characteristics (d’-value = 1.62). Regarding the perceived flavor, “cocoa aroma” was cited as significantly higher for the chocolate produced from microwave roasted cocoa beans (n = 112) compared to chocolate produced from convection roasted cocoa beans (n = 100) by consumers. Both preference and willingness to buy were higher, though insignificant at a 5% level, for the microwave roasted chocolate. A final potential benefit (studied in this research) of microwave roasting cocoa beans is the reduced energy consumption, which was estimated at 75%. Taking all these results together, the microwave roasting of cocoa is shown to be a promising alternative to convection roasting.