Conservation agriculture (CA), comprising minimum soil disturbance, retention of crop residues and crop diversification, is widely promoted for reducing soil degradation and improving agricultural sustainability. It is also claimed to mitigate climate change through soil carbon sequestration: we conducted a meta-analysis of soil organic carbon (SOC) stock changes under CA practices in two tropical regions, the Indo-Gangetic Plains (IGP) and Sub-Saharan Africa (SSA), to quantify this. In IGP annual increases in SOC stock compared to conventional practice were between 0.16 and 0.49 Mg C ha−1 yr−1. In SSA increases were between 0.28 and 0.96 Mg C ha−1 yr−1, but with much greater variation and a significant number of cases with no measurable increase. Most reported SOC stock increases under CA are overestimates because of errors introduced by inappropriate soil sampling methodology. SOC increases require careful interpretation to assess whether or not they represent genuine climate change mitigation as opposed to redistribution of organic C within the landscape or soil profile. In smallholder farming in tropical regions social and economic barriers can greatly limit adoption of CA, further decreasing realistic mitigation potential. Comparison with the decreases in greenhouse gas emissions possible through improved management of nitrogen (N) fertilizer in regions such as IGP where N use is already high, suggests that this is a more effective and sustainable means of mitigating climate change. However the mitigation potential, and other benefits, from crop diversification are frequently overlooked when considering CA and warrant greater attention. Increases in SOC concentration (as opposed to stock) in near-surface soil from CA cause improvements in soil physical conditions; these are expected to contribute to increased sustainability and climate change adaptation, though not necessarily leading to consistently increased crop yields. CA should be promoted on the basis of these factors and any climate change mitigation regarded as an additional benefit, not a major policy driver for its adoption.