Conservation agriculture (CA), with reduced tillage, permanent soil cover and diversified cropping systems, is advocated in southern Africa to improve soil quality, reduce input costs and mitigate climate-induced risks. However, improvements in terms of yield and soil organic carbon (SOC) under CA are slow and variable and many small-scale farmers are unable to buffer themselves against potential short-term financial losses. In this study we examined the effects of CA-related management practices on SOC sequestration and productivity at two medium-term sites on a sandy soil (eight year trial) and clay soil (six years) in maize producing areas of South Africa. Using field data, current input costs and market prices for crops, we calculated the gross margin for each system. Treatments compared conventional ploughing under maize monoculture with reduced tillage, intercropping and crop rotation. On the clay soil, SOC was increased under reduced tillage (57.6 t C ha−1) compared to conventional tillage (54.9 t C ha−1) while there was no difference for the sandy soil (19.7 t C ha−1 average across treatments). Profitability was most strongly influenced by seasonal rainfall, but was higher on the sandy soil than the clay soil, with an average gross margin of R11,344 ha−1 and R5,686 ha−1, respectively. This study has demonstrated that while certain CA practices can create site-specific benefits for farmers, it is highly dependent on local weather and soil conditions. For the clay soil an additional payment scheme would be required to reward farmers in southern Africa for C-sequestration to make CA profitable and achieve increased C-mitigation through soil sequestration.