Fermentation is a key step in obtaining fine cocoa through the formation of potent aroma precursors. The fermentation level of cocoa beans is traditionally assessed by measuring the amount of ammonia nitrogen (NH3) using the time-consuming Conway technique. Near infrared spectroscopy (NIRS), a rapid and efficient tool, was used to analyze NH3 levels in several hundred cocoa samples at different fermentation levels from six geographical origins. Fermentation levels were expressed as the number of fermentation days and sum of temperatures. The correlation between Conway results and NIRS spectra enabled the development of a reliable and accurate NIRS calibration to determine NH3 content. We confirm that NH3 is produced during fermentation and its amount depends on the fermentation time, sum of temperatures and geographical origin. NIRS could be used by chocolate manufacturers as a routine method to sort cocoa samples according to their level of fermentation.