The objective of this study was to evaluate the effects of storage time and bottle color on the phenolic compound profiles of Syrah red and sparkling Moscatel wines stored for 12 months in green, amber, and clear bottles. The profile of the phenolic compounds and their antioxidant activity in vitro were determined. Commercial wines were bottled in an automatic filling machine and closed with natural cork. After the bottling process, the wines were stored vertically on shelves which received natural light indirectly (±8 h/day), at temperatures which varied from 24 to 30 °C and relative humidity 40–65%. The wines were analyzed every three months over one year. Several phenolic compound families were quantified through reversed-phase high performance liquid chromatography (RP-HPLC) coupled to diode-array detection (DAD) and fluorescence detection (FD). The different bottle colors studied had not influenced the evolution of the sparkling Moscatel and Syrah red wines. The main variations obtained were related to storage time. The main changes were observed in the Syrah wine, where storage time was associated with an increase in hue (h*), decrease in catechin and epicatechin, and most notably, a decrease in the anthocyanin malvidin 3-glucoside. The sparkling Moscatel wine did not show important changes in most phenolic compounds; however, the catechin increased significantly during storage and this increase was similar in bottles of all colors. In general, the wines were stable in relation to the antioxidant activity in vitro.