Intercropping leek (Allium porrum L.) and celery (Apium graveolens L.) was recognized as an option to reduce growth and reproductive potential of weeds while maintaining yield and product quality of both crops on a high level. To optimise the intercropping system for yield, quality and weed suppression a combined use of mechanistic and descriptive models, together with experimental work, was applied. An eco-physiological model was used to improve understanding of interplant competition based on physiological, morphological and phenological processes. The model was parameterised based on characteristics of the plants in monocultures and its performance was evaluated for the crop mixtures using experimental data from different growing seasons. After validation the model was used to simulate biomass production and quality of leek, celery and seed production of Common Groundsel (Senecio vulgaris L.) for a wide range of crop densities and times of weed emergence. In a second step, the results of the simulations where summarized using a descriptive hyperbolic yield-density model, which then allowed evaluation of the intercropping system in terms of productivity, product quality, and the ability to suppress weeds. The paper will explain this combined modelling approach and how it was used to design and optimise the leek-celery intercropping system. Moreover, this study shows that functional biodiversity, as represented by the intercropping system, can contribute to the improvement of the economical potential while increasing the sustainability of highly developed agricultural production systems.