The process-based model Daisy simulates complex crop traits in different environments through various process descriptions for water and solute/nitrogen transport and crop growth of diverse agroecosystems and managements. Daisy runs in one or two dimensions, in the field (basic management unit) or several fields (distributed mode). An important aspect influencing the accuracy of the phenotype simulations is the choice of environment(s) used for parameterization, which should capture the heterogeneity in the target population of environments. Uncertainty and sensitivity analyses improve the differentiation between well predictable (repeatable) from badly predictable crop traits under genotype × environment × management interactions. Alongside history of the model and the most important applications, challenges and opportunities are presented through the need for diverse experimental data needed for parameterisations of major crops and less known or minor crops. Finally, Daisy is part of high-performance data-driven modelling platform for developing agricultural systems with minimum environmental impacts.