In a context of climate change and soil and water resource degradation, it becomes increasingly important to reduce the need for high nutrient, water, or pesticides inputs, leading to more sustainable agricultural practices. In this context, our aim is to select the best performing crops in various deleterious abiotic environments, having both a higher yield and a better quality, a better environmental « efficiency ». Because plants interact with numerous and diverse microorganisms, especially in the soil volume surrounding roots, called rhizosphere, plant-microorganism relationships in the rhizosphere is also of great agronomical and ecological importance. To address these challenges, high-throughput, non-invasive systems/methods have been developed to characterize the numerous phenotypic traits involved. Associated methods will be shortly described. Examples arising from various ongoing projects will demonstrate how shoot, root or fruit phenotyping can be applied to various thematic and crops to identify either elite genotypes face to a given abiotic stress (e.g. iron chlorosis, drought stress or nutrient deficiency), follow fruit development or identify plant and microorganism beneficial interactions.