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In the context of limiting global warming, the seagrass Posidonia oceanica (L.) gained the centrality of several international climate change mitigation projects being the most effective carbon storage sink among Mediterranean seagrasses. To assess and monitor the change of environmental conditions and economic values of natural resources, the present study moves from the insights of the System of Environmental-Economic Accounting – Ecosystem Accounting to assess the economic value of the carbon sequestration and storage capacity of the Mediterranean-endemic seagrass P. oceanica at the Tremiti Islands Marine Protected Area. The economic value is compared across: i. the reference study by Pergent-Martini et al.; ii. the ecological condition-based approach; and iii. the unit value transfer. Based on the obtained outcomes, an ecosystem-based approach would prevent biases in the accounting of the ecosystem-service provision capacity of P. oceanica and help the policy maker to implement adequate public investment policies to mitigate its overall degradation. • Carbon storage capacity is investigated as pilot by ecosystem condition-based approach for accounting purposes. • An ecological approach offers a value added to the assessment of ecosystem services. • An evaluation in biophysical and economic terms of the carbon storage of the P. oceanica is considered. • An ecological approach reduces biases to assess the economic value of the ecosystem services. • The approach helps the policy maker with efficient strategies for public spending. [ABSTRACT FROM AUTHOR]