Melatonin (MT) presence in higher plants was recently discovered and the knowledge of its function in vivo is limited. Several studies have recently shown the occurrence of MT and related compounds in grapes and wines. The analysis of MT in plants and foods represents a highly challenging task due to its wide concentration range, the difficulty in the selection of the extraction solvents because of its amphipathic nature, and the fact that it reacts quickly with other matrix components. Thus, sample processing factors; preparation/cleanup procedures; and chromatographic/detection parameters, such as HILIC and reverse phase (C8 and C18) chromatographic modes, ESI, and atmospheric pressure chemical ionization (APCI) in both negative and positive modes were evaluated. Taken together, we have demonstrated that optimal conditions were quite different for each of the matrices under study. A sonication-mediated extraction step was necessary for grape skin (100% v/v methanol) and plant tissues (50% v/v methanol), while wine and must required a SPE preconcentration step. HILIC-(+) APCI ionization was better for MT standards, while C8-(+) APCI was the best choice for grape skin and C18-(+ESI) was suitable for wine. On the other hand, C8-(+)ESI was the most appropriate for vegetal tissues of Arabidopsis thaliana. Proposed methods were validated and the LODs were in the low picogram levels range. The optimized approaches were applied to the determination of MT and its isomer in different vegetal/food samples; levels found within the range: 4.9-440 ng/g.