Multi-criteria decision analysis and cost-benefit analysis, either individually or in combination, have been used as the preferred tools to develop ecosystem services valuation, presenting significant discrepancies and variations between the calculated values. To counteract this problem, a new framework was developed based on a hierarchical weighting of the non-provisioning ecosystem services, using biodiversity as the reference ecosystem service since it is the easiest to apprehend. Their monetisation was made using the average price of EU carbon dioxide emission allowances during 2019 and 2020, obtaining reasonable and comparable results in line with what was expected for the study region. However, the revised EU Emissions Trading System Directive, which will apply from 2021–2030, generated a price escalation of carbon allowances, making it necessary to adjust or rethink the proposed framework. To achieve this goal, the paper proposes the introduction of new vectors or “missing ecosystem services” to counterbalance efforts to eliminate carbon dioxide emissions without necessarily removing humans from the equation: welfare and human health. As the linkages regarding ecosystem health, ecological restoration and human health are not well known, only welfare was incorporated into the framework. The results were highly satisfactory, in line with what was expected for the study region and the ones obtained before the price escalation of carbon allowances that started in 2021.