A transition towards an organic food system is taking place around the world. This process is favored by growing consumer demand, who associate organic crops with being healthier, tastier, and safer for the environment than conventional crops. Citrus is one of the most widely produced crops worldwide and has important socio-economic and cultural significance in the Mediterranean area. The aim of this work is twofold; on the one hand, it reveals the variability of a set of physical–chemical and nutritional quality parameters of two citrus fruit varieties, ‘Navelina’ oranges and ‘Clemenules’ mandarins, from organic and conventional production in a long-term study. On the other hand, taking advantage of the large number of results, a model is proposed that allows the successful differentiation of citrus fruits from organic and conventional production and a tool that allows predicting the production system of citrus fruits. The results suggest that organically produced citrus fruits do not generate differences in terms of external aspects, providing fruits that are acceptable to the market. Organic production techniques influenced the lower peel content and higher pulp and juice content in ‘Navelina’ orange and ‘Clemenules’ mandarin fruits and led to a greater ability to synthesize vitamin C in the juice, more essential oils in the skin, and higher seed numbers, although in all cases, the fruits can be classified as having low seed numbers. Two discriminating equations were obtained that use easy-to-measure parameters to successfully classify organic citrus fruits. The classification and prediction models obtained constitute useful tools to help in the control of the purity/authenticity of organic citrus fruits.
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