In the present study, the leaves of Manilkara zapota (L.) P. Royen (Sapotaceae), an evergreen tree recognized for its medicinal properties in Southern Mexico, were used as a model to study the effect of different drying temperatures on its metabolic profile and therefore, its antioxidant potential. For this purpose, a methanol extraction of leaves dried at room temperature (25 °C) or by heat convection (50, 75 and 100 °C) were compared in terms of drying efficiency, yield of extraction, total phenol content, 1H-NMR metabolic profile, and DPPH antioxidant activity. The drying curves enabled the fact to be uncovered that drying efficiency improves with increase of temperature, as does the level of total phenols and antioxidant activity. A metabolomics approach using principal component analysis (PCA) and orthogonal projections to latent structures discriminant analysis (OPLS-DA) of the corresponding 1H-NMR profiles allowed the impact of the drying temperature on their metabolic profile to be documented and also, caffeic acid and epicatechin as main secondary metabolites contributing to the antioxidant activity of M. zapota to be identified.