Mapping the production of Ecosystem Services (ES) is imperative for sustainable ecosystem management. Likewise, incorporating expert knowledge enhances ES research. Here, we calculate eight multi-temporal ES indicators for mainland Portugal using a spatial modelling approach. These indicators are then integrated into the novel ASEBIO index—Assessment of Ecosystem Services and Biodiversity—which depicts a combined ES potential based on CORINE Land Cover, using a multi-criteria evaluation method with weights defined by stakeholders through an Analytical Hierarchy Process (AHP). Outputs from the modelling show how ES have changed in Portugal in relation to land use changes, including trade-offs between 1990 and 2018. The composed ASEBIO index is compared against the stakeholders’ valuation of ES potential for the year 2018. The results reveal a significant mismatch between the ES potential perceived by stakeholders and the models, with stakeholder estimates being 32.8% higher on average. All the selected ES were overestimated by the stakeholders. Drought regulation and erosion prevention have the highest contrasts, while water purification, food production and recreation are the most closely aligned among both approaches. Providing the first national overview about the status of multiple ES over a 28 year-period, our findings highlight potential disparities between data-driven and stakeholder-based evaluations. Therefore, we suggest the need for integrative strategies that consider scientific models with expert knowledge for more effective ES assessments and land-use planning. This approach could help bridge the gap between data-driven models and human perspectives, resulting in more balanced and inclusive decision-making.