On the request of decision-makers, the Life Cycle Assessment (LCA) framework is increasingly applied in agri-food value chains in developing countries under particularly demanding constraints. Based on the cradle-to-farm-gate LCA results of the tomato in Rwamagana district in Rwanda commissioned by the European Union, the main objectives of the paper were to validate statistically the differences in environmental impacts among expert-based types for this crop based on location and season and identify the key-drivers of these impacts. The study was developed thanks to two intensive field visits and a survey of 15 plots. The functional unit was one kg of tomato at farm-gate. Combining several statistical analyses allowed identifying three groups of plots with contrasting input profile and eco-efficiency. For most impact categories, the first group with mainly plots in marshland during wet season had the lowest impacts and the third group with plots in hillside showed the highest impacts. The yield of tomato being significantly different between marshland and hillside plots was an important driver of these results. The second group composed of plots in marshland during the dry season generally showed intermediate impacts due to the withdrawing of water for irrigation. The second group obtained a higher freshwater ecotoxicity due to a more intensive use of toxic insecticides. The factorial analysis for mixed data (FAMD) confirmed the importance of the location and the season for the eco-efficiency of tomato plots and the hierarchical clustering on principle components (HCPC) separated the tomato plots into three clusters. The generalized linear models (GLMs) validated the differences in the environmental impacts per kg of tomato between the clusters. The principal component analysis (PCA) combined to GLM revealed that only the use of water was significantly different between the three groups. Compared to existing datasets, all groups showed high freshwater ecotoxicity i