The commercial asset value of sequestered forest carbon is based on protocols employed globally; however, their scientific basis has not been validated. We review and analyze commercial forest carbon protocols, claimed to have reduced net greenhouse gas emissions, issued by the California Air Resources Board and validated by the Climate Action Reserve (CARB-CAR). CARB-CAR forest carbon offsets, based on forest mensuration and model simulation, are compared to a global database of directly measured forest carbon sequestration, or net ecosystem exchange (NEE) of forest CO2. NEE is a meteorologically based method integrating CO2 fluxes between the atmosphere, forest and soils and is independent of the CARB-CAR methodology. Annual carbon accounting results for CAR681 are compared with NEE for the Ameriflux site, Howland Forest Maine, USA, (Ho-1), the only site where both methods were applied contemporaneously, invalidating CARB-CAR protocol offsets. We then test the null hypothesis that CARB-CAR project population data fall within global NEE population values for natural and managed forests measured in the field; net annual gC m−2yr−1 are compared for both protocols. Irrespective of geography, biome and project type, the CARB-CAR population mean is significantly different from the NEE population mean at the 95% confidence interval, rejecting the null hypothesis. The CARB-CAR population exhibits standard deviation ∼5× that of known interannual NEE ranges, is overcrediting biased, incapable of detecting forest transition to net positive CO2 emissions, and exceeds the 5% CARB compliance limit for invalidation. Exclusion of CO2 efflux via soil and ecosystem respiration precludes a valid net carbon accounting result for CARB-CAR and related protocols, consistent with our findings. Protocol invalidation risk extends to vendors and policy platforms such as the United Nations Program on Reducing Emissions from Deforestation and Forest Degradation (REDD+) and the Paris Agreement. We suggest that CARB-CAR and related protocols include NEE methodology for commercial forest carbon offsets to standardize methods, ensure in situ molecular specificity, verify claims of carbon emission reduction and harmonize carbon protocols for voluntary and compliance markets worldwide.