The data set describe variables collected from a French (N 48.84°, E 1.95°) field trial, over a twelve-year period (2009-2020), in which four innovative cropping systems designed to reach multiple environmental and production goals were assessed. Both biotic and abiotic variables were measured. In a previous data paper, we focused on nitrogen (N) fluxes collected from two systems, over eight years (2009-2016).

In the present one, we enlarge the scope of the variables, including more crop descriptions and environmental indicators, from the all four systems, and over a longer period (2009-2020). The biotic data are: growth stages, aboveground plant N content and biomass collected at different growth stages according to the species, yield components of all the crops, yield harvested with a combine machine, crop sequences. No weed, crop disease, and pest’s data are described. The abiotic data are soil physical and chemical properties (i.e. texture, calcareous content, pH, organic carbon (C) contents, and N contents) collected at different assessment periods. All agricultural practices and climate were regularly recorded, and the treatment frequency indexes and the energy consumptions were computed. The four innovative cropping systems were designed with new combinations of agricultural practices; they differed in terms of pesticide uses, N inputs, tillage practices, and crop sequences. These data could be used for benchmark to design low-input systems, to improve models for parameterization and validation, and to increase the predictive accuracy of models of growth and development for crops, specifically orphan species as linseed, faba bean of hemp, and soil C and soil N fluxes in original conditions.