There is a lack of basic knowledge about the effects of environmental factors on the concentration of secondary metabolites in fruits and vegetables. While metabolic pathways are increasingly better described, the effects of environmental factors remain insufficiently understood and quantified. The objective of this presentation is to review the major hypotheses about the effect of environmental factors on biosynthesis and accumulation of carotenoids and polyphenolic compounds in fruits and vegetables, with the exception of quality of light. Firstly, the primary and the secondary metabolisms are interlinked. Biosynthesis of carotenoids and polyphenolic compounds depends on the carbon status. Secondly, it is now well-established that secondary metabolites play a key-role in adaptation of plants to environmental constraints. More specifically, observations strongly suggest that biotic and abiotic constraints may influence the synthesis of carotenoids through the mediation of Reactive Oxygen Species (ROS). All these hypotheses and the prospects of modelling are presented and discussed from a controlling point of view with our objective being to design innovative cropping techniques for farmers in developed and developing countries which will help them to produce fruits and vegetables with enhanced concentrations in phytochemicals without resorting to GMO. The idea is discussed that organic farming results in fruits and vegetables with increased concentrations in polyphenolics, and possibly carotenoids, contributing to health benefits, because they are more stressed.