This dataset contains measurements of soil carbon decomposition and nitrogen mineralization from 36 soils in the Marsden agroecosystem diversification experiment. Soil samples were collected in fall 2021 from a long-term experiment initiated in 2002 at Iowa State University's Marsden Farm. The dataset includes laboratory data on soil organic carbon (SOC) content, soil total nitrogen content, the carbon-to-nitrogen ratio of soil, time-series CO2 fluxes from SOC decomposition in a 13.5-month lab incubation, and soil nitrogen mineralization rates. It also provides model simulations of SOC decomposition from different carbon pools using three process-based models: the Agricultural version of the Integrated Biosphere Simulator (Agro-IBIS), CN-SIM, and the Microbial-ENzyme Decomposition (MEND) models.