Climate change mitigation policies concerned with the preservation of forest carbon stocks have increasingly fuelled conflict over access to forests with traditional shifting cultivators, who have been blamed to be among the central causes of greenhouse gas (GHG) emissions from deforestation. This paper addresses the adequacy of current carbon accounting practices for shifting agriculture and potential alternatives from a complex socio-ecological systems perspective. It is argued that from such a broader perspective, the currently predominant focus on plot-based changes in total ecosystem carbon stocks, such as through forest carbon accounts, is inadequate to assess systemic climate pressures resulting from different land use systems. Such proxies represent only a single snapshot of a comparatively small land area, which however is embedded into the larger spatial and temporal dynamics of not only land use but also livelihood systems. Hence, currently predominant assessment practices are too reductionist to grasp the wider system dynamics and to provide a reliable understanding that could support policies targeting a transition away from shifting agriculture. They further run danger of replacing democratic decision-making over socioenvironmental futures with technical discussion on how to achieve rather abstract carbon values that lack political legitimacy on the ground. Policies based on such accounts are therefore not only politically contentious, fuelling conflict over access to forests, but further can be ineffective and sometimes even counterproductive for their initial objective of climate change mitigation.