There have been increased interest to propagate Moringa oleifera because of its multipurpose uses. However there are still no appropriate guidelines for long-term storage of Moringa seed because diverse results are reported in literature. Although progress has been made to understand the causes of seed deterioration, few studies have been made on natural long-term aging of seed. This study aimed to determine and compare the level of polyphenols, flavonoids, MDA and antioxidant capacity in Moringa seed stored in paper and aluminum bags at − 19°, 4°, 20° and 30 °C for 24 months as well as to investigated the relationship between these secondary compounds and Moringa seed viability. Seeds were evaluated in regular intervals of 6 months. There was minor difference between viability percentage of seed stored below 20 °C. Significant decline in viability was recorded in seed stored for 24 months in aluminum bags at 30 °C as a result of high moisture content (8%) and high temperature at which seed were exposed; While Seed stored at 30 °C in paper bags had low moisture content (5%) and retain a high viability percentage. Storage duration was the main factor affecting the changes on polyphenols and antioxidant activity levels. Although storage duration played a major role on the change in flavonoid and MDA content, the influence of storage temperature and the seed moisture content was also evident on some treatments. The change in investigated secondary compounds in seed did not always reflect on its viability percentage, but two relationships emerge from this study: The lowest moisture content, slow increase in MDA content, the lowest flavonoids content and the highest germination % in seed stored in paper bags at 20 and 30 °C at 24 months; and the highest MDA content, highest increase in flavonoids and lowest viability percentage observed in seed stored in aluminum bags at 30 °C for 24 months. It is recommended that for long-term storage (≥ 12 months) Moringa seed be stored with low moisture content (≤ 5%) at constant temperature below 30 °C.