Sustainability of agricultural practices is one of the most important issues in organic agriculture and its assessment is crucial. To this aim, evaluating the balance between the energy inputs and outputs in crop rotations could be a valuable tool. Therefore, we compared different management strategies in a four-year organic cropping system, by estimating the energy balance of crop production. Two different living mulches with no-till (B1) and green manure (B2) were compared with a cropping system without cover crop (B3), performing both energy analysis and energy balance. Energy parameters were also evaluated. The energy input of fertilizers and water was more than 55% of the total energy required by the cropping systems, suggesting that these agronomic practices should be tailored by farmers to decrease total energy inputs. The potential energy output was significantly higher in the B1 than the B2 and B3 cropping systems (20% and 54%, respectively). Results indicated that B1 and B2 could enhance the energy outputs without negatively affecting the energy consumption, since these cropping systems also showed higher energy efficiency. The introduction of the cover crop as living mulch combined with no-till could be a powerful tool to enhance systems sustainability, without compromising the crop yields.