Ecological intensification, based on agricultural practices that promote ecosystem services, has been recently proposed to match crop yield and environmental concerns. Two-year experiments were conducted in a Mediterranean environment. The treatments were: (i) four intensification levels (common vetch (CV), ryegrass (RG), bare soil without Nitrogen (N) fertilization (Control-N0) and with 100 kg ha−1 of N fertilization (Control-N100) applied during pepper cultivation), and(ii) two soil tillage [soil tillage at 15 cm and 30 cm of soil depth (ST-15 and ST-30, respectively)]. The field experiment was disposed in a randomized block design with three replications. Cover crop, soil samples, and pepper samples were collected for analysis. Soil available nitrogen increased after soil tillage, especially in CV, which showed the highest fruit yield. The reduced soil N availability in RG decreased fruit yield and N uptake. The agro-physiological efficiency of pepper was similar in common vetch and Control-N100, while it was low in ryegrass. However, the adoption of RG increased the soil organic matter more than both control treatments, which, in turn, caused a depletion of soil organic matter. Moreover, reduced tillage practices for green manuring that both cover crops arepreferable to reduce external inputs in terms of fuel saving and farming operations.