Purpose Knowledge regarding environmental impacts of agricultural systems is required. Consideration of uncertainty in life cycle assessment (LCA) provides additional scientific information for decision making. The aims of this study were to compare the environmental impacts of different growing cherry tomato cultivation scenarios under Mediterranean conditions and to assess the uncertainty associated to the different agricultural production scenarios. Materials and methods The burdens associated to cherry tomato production were calculated and evaluated by the LCA methodology. The functional unit (FU) chosen for this study was the mass unit of 1 t of commercial loose cherry tomatoes. This study included the quantitative uncertainty analysis through Monte Carlo simulation. Three scenarios were considered: greenhouse (GH), screenhouse (SH), and open field (OF). The flows and processes of the product scenario were structured in several sections: structure, auxiliary equipment, fertilizers, crop management, pesticides, and waste management. Six midpoint impact categories were selected for their relevance: climate change, terrestrial acidification, marine eutrophication, metal depletion, and fossil depletion using the impact evaluation method Recipe Midpoint and ecotoxicity using USEtox. Results and discussion The structure, auxiliary equipment, and fertilizers produced the largest environmental impacts in cherry tomato production. The greatest impact in these stages was found in the manufacture and drawing of the steel structures, manufacture of perlite, the amount of HDPE plastics used, and the electricity consumed by the irrigation system and the manufacture and application of fertilizers. GH was the cropping scenario with the largest environmental impact in most categories (varying from 18 and 37% higher than SH and OF, respectively, in metal depletion, to 96% higher than SH and OF, in eutrophication). OF showed the highest uncertainty in ecotoxicity, with a bandwidth of 60 CTUe and a probability of 100 and 99.4% to be higher than GH and SH, respectively. Conclusions The LCA was used to improve the identification and evaluation of the environmental burdens for cherry tomato production in the Mediterranean area. This study demonstrates the significance of conducting uncertainty analyses for comparative LCAs used in comparative relative product environmental impacts.