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Forest carbon sequestration offset protocols have been employed for more than 20 years with limited success in slowing deforestation and increasing forest carbon trading volume. Direct measurement of forest carbon flux improves quantification for trading but has not been applied to forest carbon research projects with more than 600 site installations worldwide. In this study, we apply carbon accounting methods, scaling hours to decades to 28-years of scientific CO2 eddy covariance data for the Harvard Forest (US-Ha1), located in central Massachusetts, USA, establishing commercial carbon trading protocols and applications for similar sites. We illustrate and explain transactions of high-frequency direct measurement for CO2 net ecosystem exchange (NEE, gC m−2 year−1) that track and monetize ecosystem carbon dynamics in contrast to approaches that rely on forest mensuration and growth models. NEE, based on eddy covariance methodology, quantifies loss of CO2 by ecosystem respiration accounted for as an unavoidable debit to net carbon sequestration. Retrospective analysis of the US-Ha1 NEE times series including carbon pricing, interval analysis, and ton-year exit accounting and revenue scenarios inform entrepreneur, investor, and landowner forest carbon commercialization strategies. CO2 efflux accounts for ~45% of US-Ha1 NEE, or an error of ~466% if excluded; however, the decades-old coupled human and natural system remains a financially viable net carbon sink. We introduce isoflux NEE for t13C16O2 and t12C18O16O to directly partition and quantify daytime ecosystem respiration and photosynthesis, creating new soil carbon commerce applications and derivative products in contrast to undifferentiated bulk soil carbon pool approaches. Eddy covariance NEE methods harmonize and standardize carbon commerce across diverse forest applications including, a New England, USA regional eddy covariance network, the Paris Agreement, and related climate mitigation platforms.