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Traditional healthcare system depends majorly on natural medicinal plants from the environment. These plants produce secondary metabolites which confer on them the various medicinal properties; however, Seasonal fluctuations have impact on their availability and quantity hence their therapeutic efficacy. This study was carried out to evaluate the effect of seasonal changes on the quantity of secondary metabolites from Neem and Eucalyptus plants. Leaves and bark of Neem and Eucalyptus plants from SHESTCO, Federal Capital Territory (FCT), Abuja, Nigeria, were collected during the four quarters of the year 2019. Samples were dried, milled into powder, quantity of secondary metabolites was estimated and antioxidant activity was analysed using standard methods and protocols. Results from this study showed a variation in secondary metabolite compositions in response to seasons. In both plants’ organs, saponin content peaked and crashed during the second and fourth quarters of the year respectively, while alkaloid had the highest content during the fourth quarter of the year. Highest level of tannin was recorded in the leaf and bark of the plants during the third quarter of the year. Antioxidant activity of both plant extracts showed a regular patterned decrease with increasing concentration, with lowest antioxidant activity for both plants’ organs recorded during the third quarter. Findings of the study indicate that the quantity of inherent secondary metabolites in the medicinal plants and their corresponding antioxidant activity varies in specific manners at different times of the year due to seasonal variation.