Coffee is the most popular soft drink in the world. Two botanical species of coffee are important for the world market and differ not only in their area of cultivation but also their components. Coffee contains more than 850 aromatic compounds which constitute its taste and flavour.Also, the method selected for the processing from the harvested cherry to the bean, the roasting profile, and the method of brewing are relevant. In this work, liquid chromatography tandem-mass-spectroscopy (LC-MS/MS) is used to investigate how the processing method influences selected aromatic compounds. Thus, three different processing methods differing in the amount of water needed for separating the coffee beans from the cherries, and two cultivars were compared. The results showed slightly higher concentrations of the caffeine and chlorogenic acid components in coffee processed with less water (the eco-pulper method). Apart from a reduced sucrose concentration, we found no significant difference in other important compounds (acrylamide, niacin, citric acid and vanillin) when plenty of water was used. Taking the investigated compounds as quality markers, the eco-pulper method is the best choice among the processing methods, especially since it conserves water, which could therefore significantly contribute to a sustainable cultivation of coffee.