This dataset provides an estimate of soil organic carbon (SOC) in the top one meter of soil across Mexico at a 90-m resolution for the period 1999-2009. Carbon estimates (kg/m2) are based on a field data collection of 2852 soil profiles by the National Institute for Statistics and Geography (INEGI). The profile data were used for the development of a predictive model along with a set of environmental covariates that were harmonized in a regular grid of 90x90 m2 across all Mexican states. The base of reference was the digital elevation model (DEM) of the INEGI at 90-m spatial resolution. A model ensemble of regression trees with a recursive elimination of variables explained 54% of the total variability using a cross-validation technique of independent samples. The error associated with the predictive model estimates of SOC is provided. A summary of the total estimated SOC per state, statistical description of the modeled SOC data, and the number of pixels modeled for each state are also provided.