Coffee is a beverage that is consumed due to its flavor and fragrance. In this investigation, we demonstrated the relations between different dry fermentation processes of coffee (aerobic, anaerobic, and atmosphere modified with CO2) and fermentation times (0, 24, 48, 72, and 96 h), with pH, acidity, and seven volatile marker compounds of coffee. Volatile compounds were extracted by solid phase microextraction (SPME) and an analysis was performed by gas chromatography–mass spectrometry (GC–MS). A significant effect (p < 0.05) between the fermentation time and a decrease in pH was demonstrated, as well as between the fermentation time and increasing acidity (p < 0.05). Acetic acid was positively correlated with the fermentation time, unlike 2-methylpyrazine, 2-furanmethanol, 2,6-dimethylpyrazine, and 5-methylfurfural, which were negatively correlated with the fermentation time. The aerobic and anaerobic fermentation treatments obtained high affinity with the seven volatile marker compounds analyzed due to the optimal environment for the development of the microorganisms that acted in this process. In contrast, in the fermentation process in an atmosphere modified with CO2, a negative affinity with the seven volatile compounds was evidenced, because this gas inactivated the development of microorganisms and inhibited their activity in the fermentation process.