The goal of this paper is to assess the relative impacts of pest-control methods in greenhouses, based on current LCA tools. As a case study, the relative impacts of two tomato production methods, chemical pest management (CPM) and integrated pest management (IPM), are assessed. The amount of the active ingredients applied, the fate of the ingredients in the various greenhouse and environmental compartments, the human exposure routes via the various compartments and the inherent toxicity of the ingredients were taken into account in the relative impact calculations. To assess the importance of model selection in the assessment, pesticide-specific fate and exposure factors for humans and aquatic and terrestrial ecosystems, used to aggregate pesticide emissions, were calculated with two different models: (1) the USES-LCA model, adapted in order to calculate the pesticide transfer from greenhouse air and soil to fruits, and (2) the empirical model critical surface time (CST). Impact scores have in general shown a higher level of potential contamination in greenhouses treated with CPM compared to IPM (a factor of 1.4 to 2.3). Relative impacts have been shown highly dependent on the selection of specific pesticides and crop stage development at the moment of pesticide application. This means that both CPM and IPM could be improved by a careful selection of pesticides. In order to improve the relative impact calculations, future research in pesticide transfer to food will be necessary.