Today, urban agriculture is one of the most widely used sustainability strategies to improve the metabolism of a city. Schools can play an important role in the implementation of sustainability master plans, due their socio-educational activities and their cohesive links with families; all key elements in the development of urban agriculture. Thus, the main objective of this research is to develop a procedure, in compact cities, to assess the potential installation of rooftop greenhouses (RTGs) in schools. The generation of a dynamic assessment tool capable of identifying and prioritizing schools with a high potential for RTGs and their eventual implementation would also represent a significant factor in the environmental, social, and nutritional education of younger generations. The methodology has four-stages (Pre-selection criteria; Selection of necessities; Sustainability analysis; and Sensitivity analysis and selection of the best alternative) in which economic, environmental, social and governance aspects all are considered. It makes use of Multi-Attribute Utility Theory and Multi-Criteria Decision Making, through the Integrated Value Model for Sustainability Assessments and the participation of two panels of multidisciplinary specialists, for the preparation of a unified sustainability index that guarantees the objectivity of the selection process. This methodology has been applied and validated in a case study of 11 schools in Barcelona (Spain). The social perspective of the proposed methodology favored the school in the case-study with the most staff and the largest parent-teacher association (social and governance indicators) that obtained the highest sustainability index (S11); at a considerable distance (45%) from the worst case (S3) with fewer school staff and parental support. Finally, objective decisions may be taken with the assistance of this appropriate, adaptable, and reliable Multi-Criteria Decision-Making tool on the vertical integration and implementation of urban agriculture in schools, in support of the goals of sustainable development and the circular economy.