Fruit ripening time together with related fruit quality traits, including size, firmness, color, acidity, or soluble solid content, must be optimized to ensure a sustainable Prunus production in the new context of global warming and climate change. In this context, elucidating the molecular mechanisms controlling the fruit development is a primary target for improving Prunus species. The early developmental stages are crucial to determine fruit characteristics including size and quality. During the first weeks after the fruit set, many changes occur in the Prunus fruit, from rapid cell division to producing essential metabolites. The information on molecular events at the transcriptional, hormonal, and metabolite levels underlying fruit development in Prunus fruits has increased considerably. However, we still poorly understand the molecular switch that occurs during the transition from flowering to ripe fruits. The objective of this review was to analyze the molecular basis of the fruit development process in Prunus. We focused on the global perspective of fruit development in Prunus at morphological and molecular levels. The integrated phytohormonal, genomic, transcriptomic, metabolic, and epigenetic approach of this review will allow a better understanding of the molecular switch involved in the ripening process with important consequences from a production and breeding point of view in the context of global warming affecting Prunus production.