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Ecosystem service (ES) models can only inform policy design adequately if they incorporate ecological processes. We used the Lund-Potsdam-Jena managed Land (LPJmL) model, to address following questions for Mexico, Bolivia and Brazilian Amazon: (i) How different are C stocks and C sequestration quantifications under standard (when soil and litter C and heterotrophic respiration are not considered) and comprehensive (including all C stock and heterotrophic respiration) approach? and (ii)Howdoes the valuation of C stock and C sequestration differ in national payments for ES and global C funds or marketswhen comparing both approach?Wefound that up to 65%of C stocks have not been taken into account by neglecting to include C stored in soil and litter, resulting in gross underpayments (up to 500 times lower). Since emissions from heterotrophic respiration of organic material offset a large proportion of C gained through growth of living matter, we found thatmarkets and decision-makers are inadvertently overestimating up to 100 times C sequestrated. Newapproaches formodelling C services relevant ecological process-based can help accounting for C in soil, litter and heterotrophic respiration and become important for the operationalization of agreements on climate change mitigation following the COP21 in 2015. [ABSTRACT FROM AUTHOR]