This dataset comprises measurements related to soil carbon decomposition from different soil depths in 36 soils during a laboratory incubation experiment. These soil samples were collected from a long-term agroecosystem diversification experiment initiated in 2002 at Iowa State University’s Marsden Farm. The dataset includes laboratory-measured soil organic carbon (SOC) content, CO2 fluxes from SOC decomposition, and nitrogen mineralization rates. Additionally, it also includes model simulation results about soil carbon decomposition represented by three different process-based models: CN-SIM, Agro-IBIS, and MEND.