Microwave roasting of cocoa beans was studied as an alternative toward convection roasting. The impact of each roasting treatment was assessed based on roasting degree indicators (moisture content, color, tetramethylpyrazine/trimethylpyrazine ratio), microstructural changes as visualized by cryogenic scanning electronic microscopy (cryo-SEM) and the aroma development as determined by head space-solid phase microextraction–gas chromatography–mass spectrometry (HS-SPME–GC–MS). Time (10–50 min) and temperature (110–160 °C) were varied for convection roasting, whereas time (7–17 min) and power input (180–450 W) were altered for microwave roasting of cocoa beans. Results revealed that by selecting appropriate microwave-roasting parameters (time and power input), cocoa beans with a more pronounced brown color and lower tetramethylpyrazine/trimethylpyrazine ratio could be obtained, while having a similar moisture content compared to convection roasting. At microstructural level, differences in number and size of macropores were not directly related to the roasting technique, but were principally determined by the applied temperature or power input. Based on the aroma profile, microwave roasting resulted in a more intense cocoa aroma, compared to convection roasting. Therefore, microwave roasting could be a promising alternative technique to roast cocoa beans in a shorter processing time while creating a more intense aroma.