Antioxidant-rich food and supplements are crucial to counteract free radicals that cause oxidative stress, which is responsible for the development of several diseases. Moringa oleifera Lam. is a plant with antioxidant properties mainly attributed to its phenolic compounds and, recently, to its isothiocyanates, deriving from the hydrolysis of glucosinolates. Although this species is native to Asia, its cultivation in Paraguay can generate a differential composition in its secondary metabolites, by the warm and humid environment where it is grown. In this study, we compared the total phenolic content, the direct antioxidant activity (DPPH and ABTS cationic radical assays) and the glucomoringin content (main glucosinolate of M. oleifera and precursor of the bioactive isothiocyanate) of aqueous extracts of different parts (leaves, seeds, bark and branches) of M. oleifera, grown in Paraguay. Two different drying treatments (freeze-drying and oven drying, 40°C) were performed on the vegetal samples before extraction. We could observe that branches of M. oleifera (in both drying treatments) are a reservoir of antioxidants that can be exploited for the preparation of extracts for nutraceutical applications, together with the commonly used oven-dried leaves and freeze-dried seeds.