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This study investigated the effects of different storage times (0–24 months) and temperatures (−20 °C, 4 °C, 25 °C, and 35 °C) on the volatile compounds and color of vanilla beans from Taiwan using ISO 5565-1:1999 as the commercial quality indicators. The vanillin level was highest at −20 °C for 6 months (p < 0.05) and no color-perceived differences (ΔE < 1). At 35 °C, lipid metabolism, enzymatic oxidation, and Maillard reaction products, such as 2-acetylpyrrole and 5-hydroxymethylfurfural, were detected after 18 months of storage, leading to significant color-perceived differences (ΔE > 5) and changes in the odor profile, which did not meet ISO standards. To sum up, as the storage temperature and duration increased, oxidative metabolites increased. Furthermore, storage at −20 °C or 4 °C is stable, but considering vanillin quality, the storage temperature of −20 °C can extend the storage period by 12 months.