Jujube fruit (Ziziphus jujuba Mill.) has been a food source since ancient times. In Spain, it is considered a marginal crop, and jujube fruits are of low economic importance. Its consumption is bound to local marketplaces. However, jujube is a good alternative crop due to its climatic adaptation and low-input conditions. We aimed to evaluate the morphological, physicochemical, and bioactive compounds of jujube fruits grown under low-input conditions (wild and organic farming) in the Mediterranean basin, specifically in Marjal de los Moros, Valencia, Spain. The organic system produces higher protein, fiber, ash, and carbohydrate concentrations from small-caliber fruit cultivars. Potassium and phosphorus are the major mineral elements in jujube. The fruits’ total polyphenols range from 480.83 to 630.81 mg EGA·100 g−1 fw in organic conditions and 520.71 mg EGA·100 g−1 fw in wild conditions. Low-input conditions influence the production of glucose (sweet fruits) and bioactive compounds, as well as mineral concentrations. A strong relationship exists between vitamin C levels and the potassium concentration. Jujube fruits are classified as “vitamin C-rich”. A 20 g serving of fruit can provide the regular vitamin C requirements of an adult person. The environmental and nutritional opportunities offered by jujubes are in line with different SDGs.