The genus Citrus amounts to one of the most relevant fruit crops in the world. This work assays overall fruit quality information in order to ascertain the optimal harvest timing of three late-season orange cultivars (‘Barberina’, ‘Valencia Midknight’ and ‘Valencia Delta Seedless’) during two consecutive growing seasons. Thus, morphological and physicochemical parameters, organic acids, polyphenolic content and antioxidant activity (ABTS and DPPH) were analyzed. ‘Barberina’ yielded the highest morphological (large and heavy fruits, albeit with lower fruit color index) and physicochemical (high juice content and intermediate but optimal acidity) fruit quality, with April providing the optimal harvest timing. By contrast, ‘Valencia Delta Seedless’ offered the smallest fruits, while ‘Valencia Midknight’ reported the lowest physicochemical juice quality (low juice content and earlier sensory depreciation). Nevertheless, both ‘Valencia Delta Seedless’ and ‘Valencia Midknight’ had higher functional quality than ‘Barberina’, which could be interesting for the industry in terms of obtaining higher added value products. Thus, ‘Valencia Midknight’ fruits recorded the highest organic acids concentration, especially in citric acid, while ‘Valencia Delta Seedless’ fruits showed the highest antioxidant activity and ascorbic acid concentration. In addition, while March-April emerged as the optimal harvest timing in terms of the highest organic acids concentration and antioxidant activity, it was February the optimal harvest timing for polyphenols content. Finally, the 2017/2018 growing season proposed better response of color index, density, polyphenols and antioxidants, but lower results of total organic acids.