This study was part of a cover crop-based, organic rotational no-till cropping systems experiment conducted from 2015-2017 at Pennsylvania State University’s Russell E. Larson Agricultural Research Center in Rock Springs, PA, USA, employing a corn (*Zea mays* subsp. mays L.), soybean (*Glycine max* (L.) Merr.), spelt (*Triticum spelta* L.) rotation that is typical for feed and forage farmers in the Mid-Atlantic USA. Data include: Nitrate leaching from anion resin bags; Nitrous oxide fluxes from static chambers and isotopomers; Soil inorganic N including ammonium and nitrate; Soil moisture and temperature; Cover crop biomass as well as carbon and nitrogen content and nitrogen isotope ratios; Cash crop yields.