Soil CO2 data collected in transects across faults in the southern Malawi Rift in August 2018. Measurements of soil CO2 flux were collected during a survey in August 2018 during the dry season in Malawi, in order to attempt to reduce the possibility of a high biogenic flux obscuring the output of deeper CO2. We collected measurements using the accumulation chamber method (Chiodini et al., 1998), where a soil collar is coupled to the ground surface, and the gas flux is sampled and analysed for CO2 using a PP Systems EGM-4 Environmental Gas Analyser and a SRC-1 Soil Respiration Chamber. A high-resolution digital elevation model (DEM; 12.5 m TanDEM-X), was used to identify active fault scarps in southern Malawi (following Wedmore et al., 2020), which were the focus of our investigation. We collected flux measurements running from the footwall across the active faults and into the hanging wall of the scarps that we identified, with approximately 10-50 m spacing between individual sampling locations. Also published here is an ipython notebook to analyse the data.