Fermented coffee beans are believed to have significantly different compositions of phenolic and volatile compounds and physicochemical properties compared to unfermented coffee beans. This study evaluated the effects of fermentation on coffee beans at a commercially roasted level by characterizing their phenolic compounds and semi-quantifying their volatile compounds using liquid chromatography–electrospray ionization quadrupole time-of-flight mass spectrometry (LC-ESI-QTOF-MS/MS) and headspace/gas chromatography–mass spectrometry (HS-SPME-GC-MS). Coffee beans from two varieties of Coffea arabica, Geisha (G) and Bourbon (B), both fermented beans had higher contents of total phenolic compounds (G: 33.52 mg/g; B: 29.95 mg/g), total flavonoid (G: 0.42 mg/g; B: 0.35 mg/g), total tannins (G: 3.49 mg/g; B: 3.18 mg/g), and higher antioxidant potential in all assays. In total, 131 phenolic compounds were tentatively characterized via LC-ESI-QTOF-MS/MS, where 73 and 65 phenolic compounds were characterized from fermented Geisha and Bourbon, respectively. Regarding GC-MS, the fermented coffee beans had higher levels of phenols, pyrazines, furan, and furanic compounds. These findings substantiated that fermented coffee beans exhibit elevated levels of phenolic and volatile compounds and greater antioxidant activity, which could contribute to relatively higher nutritional values and organoleptic properties.