Fruits and vegetables are a main source of health compounds and a hedonic constituent of human diet. In the context of global change, plants will be facing increasing abiotic and biotic constraints. Therefore, innovations are expected in order to improve plant adaptation these constraints as well as to reduce water, nutrients and chemical inputs. Plant breeding, innovative cultural practices and climate control are all effective levers that can be combined in order to improve crop yield and quality in low input production systems. In this context, a renewed modeling effort is needed in order to provide an integrated understanding of horticultural system functioning. Model goals for the future are to describe the cross-talk between physiological processes at multiple plant scales, simulate complex greenhouses designs, anticipating the consequences of environmental fluctuations or pest attack for system control and management.