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Indicators of carbon storage in forests and other land uses have gained much prominence to evaluate and endorse land-based climate change mitigation policies. The outcomes of such assessments can have direct livelihood implications for dwellers living at the forest-agriculture frontier, such as shifting cultivators or subsistence farmers. This contribution critically discusses the methodological relevance of carbon stock indicators to assess long-term emission dynamics of land uses, and furthermore addresses the 'politics of measurement' that can be involved in policy practice. From a complex socio-ecological systems perspective, the paper argues that carbon stock indicators provide necessary but not sufficient information to endorse land use policies with mitigation aims. While they may indicate one-off sequestration gains through vegetation and land-use change, they cannot account for permanent hidden emissions that emerge as part of the broader agrarian transitions that accompany land-use change. Over the long term, this may render related mitigation interventions ineffective, if not counterproductive. Furthermore, carbon stock estimates for future land-use scenarios sometimes draw on biased assumptions, or are constructed within histories of discrimination, through which they may further marginalize subaltern groups such as shifting cultivators. A paradigm shift is needed that includes more integrative assessment approaches.