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Fruits represent an important component of the diet due to their unique composition in terms of vitamins, antioxidant, fibers and other compounds; these fruit-specific elements are necessary for a healthy diet and are not biosynthesized by the human body, therefore a daily fruit (and vegetable) consumption is highly recommended. To increase fruit consumption, high quality produce has to be offered to consumers together with a diversity of fruit/fruit-derived products. Generally speaking, quality parameters are affected by a number of factors including the genetic background, the responses to agronomic and environmental conditions, and the reactions to pre- and post-harvest intentional and unintentional stresses. The development of advanced protocols and tools aimed at studying on large scale the molecular and metabolic processes represents a great opportunity to elucidate mechanisms related to quality parameters and responses to stressors. The research carried out had the main goal of investigating, by means of different approaches, some molecular and biochemical features responsible for/associated with quality-related aspects of fruits belonging to the genus Prunus.