Breeding for crops in the context of climate change necessitates phenotyping tools for roots in field conditions. Such in-field phenotyping requires the development of rapid and non-destructive measurement techniques for the screening of relevant root traits under sub-optimal conditions. In this study, we used scanner-based minirhizotrons to measure in situ the root length and surface/volume densities of roots for four wheat varieties, under four different growth conditions: irrigated and rainfed coupled with optimal and sub-optimal N fertilization under a Mediterranean climate. For all the treatments, grain yield correlates with minirhizotron-based root surface density measured at anthesis (r(2) = 0.48). Irrigated and rainfed conditions led to contrasted relations between roots and grain yield: no correlation was found in irrigated plots, while under rainfed conditions and sub-optimal fertilization, the higher yields are related to a higher root colonization of the deeper soil layers (r(2) = 0.40). Shoot biomass was correlated to grain yield in irrigated conditions, but not in rainfed conditions. However, for the latter, the total root weight, the proportion of which being mainly located in the top soil, is not related to the grain yield. In this way, we show the relationship between these higher grain yields and a stress avoidance mechanism of the root system characterized by a higher root density in the deep soil layers. Thus, unlike shoot biomass measurements, scanner-based minirhizotron allows the direct detection of such a stress-related root development, and therefore opens the door to a better prediction of grain yield.