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 the fruits, 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 in the mandarin cv. Afourer, of high commercial value. The results showed a clear differentiation according to the sampling date (evolution of pollination) and some differences were found at early stages of the fruitlet development 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. This study explores how different pollination techniques affect mandarin ovaries during the pollination and early fruit development stages. Uruguayan citrus farming thrives on producing high-quality fruit, and this research investigates sustainable methods that balance fruit quality with seed reduction and increased fruit set. By using a combination of traditional and innovative methods—like confining pollinators with mesh and applying gibberellic acid—the study examines the metabolic changes in mandarin ovaries using 1H NMR. The findings reveal that different cultivation techniques influence in fruit characteristics offering insights into sustainable practices for better fruit production.