The aim of this study was to highlight the existence of a correlation between Maillard reaction and protein aggregation in bovine meat as a function of power level and exposure time used by microwave heating. The obtained results are compared with those of convective heating. For this, Fourier Transform-Infrared Spectroscopy was used to analyze the effects of microwave heating on different samples of bovine meat cooked in microwave ovens at three power levels of 700, 900 and 1100 W, and in conventional electric oven at the temperature of 170°C. An increase in intensity of methylene vibration bands after microwave cooking at 700 W for 3 min was more than that which occurred after microwave cooking at 900 and 1100 W for 2 min, showing that Maillard reaction depends on exposure time to microwaves. Also, the β-sheet contents at 1695 and 1635 cm−1 in meat samples heated for 2 min by microwave oven increased with increase in power level from 700 to 1100 W, showing that protein aggregation is strictly related to the power level of microwave heating. This result showed that an extended exposure time to microwave heating can significantly alter gastrointestinal digestive processes.