The soil organic carbon database is a harmonized and structured data set with information about soil organic carbon (SOC), soil bulk density (BD), and coarse fragments (CF). The SOC, BD, and CF data were fitted to one standard depth of 0-30 cm using a mass preservation spline implemented in R programmation language. The data was obtained from Unidad de Planificación Geográfica y Gestión de Riesgo of Ministerio de Agricultura Ganadería y Alimentación (UPGGR-MAGA), Facultad de Agronomía of Universidad de San Carlos de Guatemala (CEDIA-FAUSAC), and the World Soil Information Service (WoSIS). This database covers the entire Guatemalan territory, although its distribution does not represent all ecosystems, soil types, and coverages/land use. It contains 910 observations of SOC, 704 of them have BD information, and 8 have CF information. The entire data set has information on the year of observation, and its temporal distribution goes from 1965 to 2010. Nearly 50% is in the decade 2000-2010, and 41% is in the 2010 year. In addition, the analytical methods for quantifying SOC, BD, and CF are available in 99, 25, and 0% of the data, respectively. SOC contents range from 1.45 to 162 g*kg^-1, BD values from 0.42 to 1.69 g*cm^-3, and CF values from 0 to 21%wt.