System models help policymakers to produce net zero decarbonization pathways. In 2019, Costa Rica launched its National Decarbonization Plan (NDP) – constructed using a detailed Open-Source energy Modelling System (OSeMOSYS-CR) model and simplified ones for non-energy sectors. The country then developed an integrated Climate, Land, Energy and Water (CLEW) model to capture synergies across sectors and guide future climate related processes. This resulted in the CLEW-CR model. In 2020, the country updated its Nationally Determined Contributions (NDCs), deploying a highly participatory process supported by the CLEW-CR model to guide the discussions with over 150 stakeholders. This paper presents the framework adopted to develop the CLEW-CR model (from data collection to scenarios creation and cost-benefit analysis) and describes its use to align its NDCs with its NDP. Over 15 different scenarios were produced to inform the country's dialogue during the updating process of its NDCs demonstrating the flexibility of this model to support multiple policy questions. This paper shows that deploying the NDC by 2030 and the NDP by 2050 would result in a net economic benefit of $55 billion – about 85 % of Costa Rica's GDP, highlighting the economic viability of Costa Rica's commitment to a sustainable future.