Melatonin (MEL), long recognized as an animal hormone, has recently emerged as a crucial regulator in plants, influencing both developmental processes and responses to environmental stress. Furthermore, MEL has been associated with the regulation of sugar transporters and enzymes such as invertases and sucrose synthases, suggesting a role in fine-tuning carbohydrate partitioning. To investigate MEL’s role in non-climacteric fruit systems, exogenous MEL was applied to sweet cherries, followed by a short-term metabolomic analysis. This approach revealed a clear association between MEL application and the accumulation of specific soluble sugars, including arabinose, turanose, talose, and mannobiose. Complementary transcriptomic data showed that MEL modulates genes involved in sugar metabolism as early as 24 hours post-treatment, with sustained effects observed up to 72 hours. Sugars could play a pivotal role in postharvest physiology, not only as primary energy sources but also as signaling molecules that influence stress responses, and fruit palatability. Maintaining sugar balance during storage is critical for preserving fruit quality, consumer acceptance, and shelf life. These preliminary findings suggest that MEL may contribute to sugar homeostasis under postharvest stress, supporting energy balance and enhancing cellular resilience. Overall, melatonin emerges as a potential key metabolite that integrates environmental signals with sugar signaling networks in sweet cherry fruit.