This paper proposes a fast, accurate, and quantitative method for alkylpyrazines determination in cocoa liquors samples using gas chromatography with ion trap mass spectrometry detection (GC/IT-MS) and on-line headspace (HS) sample introduction. The optimization of the experimental conditions of the headspace gas chromatography–mass spectrometry (HS–GC–MS) system was carried out using the univariate method, aiming to find a compromise between time of the analysis, sensitivity and pyrazine resolution in a Carbowax (AV-WAX) fused silica capillary column. The procedure was validated through accuracy and precision studies. The results showed a highly satisfactory accuracy rate for the method with a relative standard deviation (RSD) during 1 day and between days of <5.0% (n=5). On the other hand, the recovery percentages (94–99%) were quantitative in all cases, with a RSD of <4.0% (n=5). Finally, the use the on-line headspace extraction step simultaneously with the analytes separation and detection of the previous sample injection increased the analysis frequency to 3 samples/h. A total of 120 cocoa liquor samples were analyzed.