One of the key challenges for ecosystem services research is to develop a comprehensive methodological approach in which biophysical, socio-cultural and monetary value-domains can be explicitly considered and integrated into decision making processes. This paper operationalizes a methodological approach for ecosystem service assessment on the basis of value pluralism. We assessed eleven ecosystem services delivered in the Doñana social-ecological system (SW Spain). We found that different ecosystem service trade-offs came into view depending the value-domain in which services were assessed. The use of different valuation methods uncovers the fact that methods to elicit value actually shape and define the values being elicited. In this context, the prevalence of biophysical and monetary value-domains in scientific literature entails two main concerns: (1) the ecosystem service concept reflect in a limited extent the concerns of their beneficiaries, and (2) ecosystem service assessment results are biased towards the information provided by markets at the expense of other value-articulating institutions. Recognizing the role of ecosystem service assessment methods as value-articulating institutions, we call for a methodological framework able to contemplate the multidimensional nature of ecosystem services.