Cocoa beans (Theobroma cacao L.) can be used for craft chocolate production, which arouses consumer interest due to their perceived better quality. This study aimed to evaluate the chemical profile of 80% artisanal chocolate samples produced with cocoa beans subjected to different maturation conditions. In the first maturation process, beans were matured under no-oxygen conditions, and in the second, the toasted beans were matured in oak barrels. The volatile compounds of the chocolate samples were extracted by the solid-phase microextraction method in headspace mode and analyzed by gas chromatography/mass spectrometer. The non-volatile compounds were extracted with methanol and analyzed through paper spray mass spectrometry. Overall, 35 volatile compounds belonging to different chemical classes (acids, alcohols, aldehydes, ketones, esters, and pyrazines) were identified, such as propanoic acid and butane-2,3-diol. In addition, 37 non-volatile compounds, such as procyanidin A pentoside and soyasaponin B, were listed. Tannins, flavonoids, and phenylpropanoids were the main chemical classes observed, varying between the two samples analyzed. Therefore, it was possible to verify that maturation conditions affected the metabolomic profile of the 80% artisanal chocolate samples, being able to influence the sensory characteristics and bioactive compounds profile. Given these results, the sensory evaluation of these chocolates is suggested as the next step.