Land consumption and climate change have intensified natural disasters in urban areas. In response to these emergencies under the European 2030 Agenda, Sustainable Development Goals have been established to improve ecosystem protection and increase resilience and adaptation to natural disasters globally (Goal 13 “Climate action” and Goal 15 “Life on land”). In order to implement governance tools appropriately, it is necessary to know the relationships among the drivers, the changes in the state of urban ecosystems and agro-ecosystems, and the impact on the supply of goods and services at spatial and temporal scales. In this paper, Land-Use and Land-Cover Changes (LULCCs) in the metropolitan area of Rome have been investigated, with the purpose of detecting the synergistic variations in the supply of the flood mitigation and agricultural production ecosystem services (ES). The methodology is based on a GIS (Geographic Information System) analysis that identifies the transformation processes and permanencies related to land-cover. The variation in flood mitigation services was quantified through the use of the Urban Flood Risk Mitigation Model (UFRM) from the InVEST (Integrated Valuation of Ecosystem Services and Tradeoffs) suite, while the variation in agricultural production through productivity coefficients was associated with changes in land-uses. Finally, an analysis of LULC-induced synergies and trade-offs between the two services was performed. The results show a net negative change in ES supply, caused mainly by urbanization at the expense of agricultural land. This decrease in ES supply is not offset by other LULCC transitions. In addition, the analysis of synergies and trade-offs between flood mitigation ES and agricultural production ES (in arable land, orchards, vineyards, and olive groves) shows that the reduction of agricultural land negatively affects both ES. The innovative contribution of this paper lies in setting an integrated methodology that is able to investigate how LULCC influences both hydraulic safety and food security. Findings can be useful to support planning of enhancing the role of agriculture in metropolitan areas.