A 2-year field trial was carried out in a climate change context on organic tomato crop. The objectives were: (1) to study the best synergistic combination of a set of agro-ecological techniques, as potential adaptation strategies in Mediterranean environment [i.e.: soil surface shaping; crop rotations; cover crops introduction (barley, vetch and their mixture); cover crop termination techniques (roller crimper—RC vs green manure—GM) and organic fertilization]; (2) to evaluate the sustainability of these techniques by assessing energetic performance. In both years, the barley-RC and mixture-RC combinations reduced weeds fresh and dry weights. In 2014, the combination of commercial organic fertilizer and vetch gave both the highest tomato marketable and total yields (26.88 and 31.97 t ha−1, respectively). In 2015, these production parameters decreased by 30.7 and 35.4%, respectively compared to 2014, and GM-cover crop produced on average more than twice as much as RC-cover crop. The cover crop termination by RC reduced soil mineral N peak than GM treatment, at full flowering in particular in plots after vetch and in the mixture plots in 2014 and 2015 respectively, thus reducing the potential environmental impact by nitrate leaching. The highest energy consuming input was fertilizers (by 57%). The highest energy efficiency and net energy were found in the vetch-GM combination (with low fertilizer input). The research points out that agronomic practices must be fine-tuned to the specific pedoclimatic condition for an efficient use of energy. Moreover, agronomic input reduction is not only feasible, but also creates environmental benefits.