Uruguayan citrus farming maintains its export competitiveness thanks to the organoleptic and health quality of its fresh fruit. The intensification of production systems drives the design of new high-efficiency sustainable technologies to improve competitiveness. In this work, the effects of the use of different agronomic techniques, compatible with beekeeping production, that allow reducing the presence of seeds, in combination with techniques that favor the increase in citrus fruit set, were evaluated. These techniques involve the use of pollinators confined by mesh and their comparison with the use of conventional technologies (exclusion of bees, application of gibberellic acid). Aqueous extracts of mandarin ovaries were evaluated throughout the pollination process (open flower, fallen petals, fruit without pistil and 6mm fruits) using 5 cultivation techniques. An untargeted metabolomic study was carried out using nuclear magnetic resonance to explain the endogenous changes that occurred during pollination and ovary development to understand the metabolic pathways involved in the parthenocarpic process of the Afourer mandarin, of high commercial value. The results showed a clear differentiation according to the sampling date (evolution of pollination) but no differences were found according to the cultivation technique. When the fruit forms, sugar metabolism is favored; however, in the early stages of pollination, important signals related to phenolic compounds were found. The different cultivation techniques showed differences in fruit production and the presence of seeds. Understanding the pollination process from a metabolic point of view will help design cultivation techniques that favor the production of quality fruit in a sustainable manner.