This study compared the regular and decaffeinated coffees in relation to antioxidant capacity, levels of some antioxidant molecules and stability of these parameters over a six-month period under different storage conditions. The regular coffee samples analyzed right after the industrial production showed higher antioxidant capacity (ORAC and DPPH), the same levels of phenolic compounds and higher levels of phenolic acids than decaffeinated coffee. After six months, the closed packs of both the grades kept under vacuum at 20°C did not show significant changes from the initial results; the open packs stored at 4°C showed small but statistically significant reductions and the open packs stored at 20°C showed higher and statistically significant losses (p < 0.05). Oxygen was the most important factor for these losses but temperature also played an important role. Tests showed that the storage conditions were very important to preserve the quality of coffees regarding the analyzed parameters.