Maize (Zea mays L.) and tomato (Solanum lycopersicum L.) are two important crops in Mediterranean countries. The objectives of this study were to evaluate the differences and similarities in energy flow between conventional and organic tomato and maize crops. Our results indicated that the total energy input in the conventional system was higher than in organic system and for individual crops was 25.90 and 29.34% higher for tomato and maize, respectively, than the organic system. Of the inputs for the different operations, fertilizers consumed the bulk of the energy for all crops. In maize crop, human labour had little impact on total energy use both in organic and conventional system. In addition, seed inputs in maize production had corresponded to 11.44% of the total energy requirement. Concerning the pesticides inputs, there were significant differences between organic and conventional systems. In both crops, the pesticides energy input was higher in conventional production compared to organic system. Moreover, irrigation inputs were 13-23% of the total energy use in the organic system and 12-20% in the conventional system. In both crops, the energy output and energy productivity were also higher in conventional production compared to organic system. Our study shows that the adoption of organic cultural system could reduce energy inputs.