Environmental benefits can be achieved by organic farming systems; however, weed pressure and timely crop nutrition remain important drawbacks for many field crops. Agroecological practices, such as double cropping (e.g., intercropping and relay cropping), using forage legume species can provide nitrogen (N) to the companion crop through biological N fixation and tackle weed issues by competing for light, water and land. The present study investigated the effect of intercropping (IC) and relay-cropping (RC) systems of durum wheat (Triticum turgidum subsp. durum (Desf.) Husn) and forage legumes (Trifolium subterraneum L., Medicago polymorpha L., and Lotus corniculatus L.) by varying organic N fertilization with the aim to reduce N-requirement and weed pressure and increase wheat grain yield and grain protein content in Mediterranean organic farming systems. N fertilizer significantly improved wheat grain yield and grain protein, while a null effect on legume and weed biomass yields was found. Double cropping (T. durum-M. polymorpha, and T. durum-L. corniculatus) enhanced wheat grain yield as compared to the control and the T. durum-T. subterraneum. IC significantly improved legume yield, grain protein and the land equivalent ratio (LER) and reduced weed dry biomass as compared with the RC and the control. Among legume species, T. subterraneum outperformed the others and was less affected by the wheat’s competitive performance. Nonetheless, M. polymorpha was as effective as T. subterraneum in controlling weeds. Weed dry biomass was linearly reduced by increasing legume yield; the relationship improved by cumulating wheat grain yield to legume yield. Overall, this study indicated that double cropping, especially IC, can be a suitable agroecological practice to tackle weed issues and reduce N-requirement in Mediterranean organic cereal-based systems.