Coffee beans contain different volatile and non-volatile compounds that are responsible for their flavor and aroma. Herein, principal component analysis (PCA) was employed to correlate the non-volatile composition of specialty and traditional coffees with drink quality. The quantified non-volatile compounds included caffeine, chlorogenic acid (3-CQA), caffeic acid, and nicotinic acid in both types of coffee samples, while 5-hydroxymethylfurfural (HMF) was only quantified in the specialty coffee samples. The most abundant compounds present in specialty coffees were associated with the aroma and flavor, affording a high drink quality. In traditional coffees, the most abundant compounds included nicotinic acid and caffeine, indicating a stronger roasting process, loss of sensory characteristics, and blended formulations. PCA showed a distinction between the traditional and specialty coffees such that a relationship between the contents of the compounds in each type of coffee, quality, and classification could be established.