Greenhouse production is the most intensive plant production system, both in terms of yield and investment and inputs. There are different alternatives of farming systems among which producers can choose. To facilitate decision-making it is convenient to develop applications that analyze the alternatives from the point of view of sustainability. The analysis of the sustainability of greenhouse production must be carried out according to the criteria that affect all the processes that make up the agri-food value chain. In this work, the criteria and sub-criteria that influence the sustainability of greenhouse production are analyzed first. Next, the alternatives in the most important cultivation system in the production of greenhouse tomatoes in the Spanish Mediterranean Basin (soil, perlite and nutrient film technique, NFT) are evaluated. The work is carried out based on the opinion of ten experts from the integrated sectors of the agrifood value chain. The results indicate that the sustainability of greenhouse production increases in the order: soil < perlite < NFT due to a higher valuation of the latter alternative in relation to commercial, natural, human, material resources and management versus economic resources.