This dataset contains a measurement of physically protected carbon (microaggregate-within-macroaggregate C) and potential drivers of physically protected C accumulation during grassland restoration. The data were collected from three independent grassland restorations from agriculture in North America and South Africa. Northeast Kansas, USA data were collected in May 2013. Northeast Free State, RSA data were collected in September–November 2005. Southeast Nebraska, USA data were collected in October 2008–May 2008. Aggregate fractionations were performed by hierarchical wet sieving (Six et al 2000). Carbon and N quantification were done by flash combustion-gas chromatography. Microbial biomass C quantification was performed with chloroform fumigation-incubation (chloroform fumigation-extraction in the case of northeast Kansas). Phospholipid fatty acid biomass analysis was conducted using the methods of Bligh and Dyer (1959).