In order to evaluate the sustainability of land and water resources, there is a need for a better understanding of the relationships between land surface characteristics and the energy and water cycles. These relationships are analysed using JULES. JULES includes the full hydrological cycle and vegetation effects on the energy, water, and carbon fluxes. This model currently only simulates land surface processes in natural ecosystems. An adapted version of JULES for agricultural ecosystems, called JULES-SUCROS has therefore been developed. In addition to overall model improvements, JULES-SUCROS includes a dynamic crop growth structure that fully fits within and builds upon the biogeochemical modelling framework for natural vegetation. Specific agro-ecosystem features such as the development of yield-bearing organs and the phenological cycle from sowing till harvest have been included in the model. This paper describes the structure of JULES-SUCROS and evaluates the fluxes simulated with this model against FLUXNET measurements at 6 European sites. We show that JULES-SUCROS significantly improves the correlation between simulated and observed fluxes over cropland and captures well the spatial and temporal variability of the growth conditions in Europe. Simulations with JULES-SUCROS highlight the importance of vegetation structure and phenology, and the impact they have on land–atmosphere interactions.