In the current context of climate change, the impact of trees in agroforestry systems is expected to mitigate water and heat stresses, particularly in semi-arid environments. Within this framework, in a two-year trial conducted at INRAE in Southern France, the dynamics of microclimatic parameters and the edaphic environment of durum wheat were investigated under a yearly-pruned (AF) and a never-pruned (AF+) 6-m apart alley olive orchard, in comparison with controls under full sun. Here it was recorded a reduction of photosynthetic active radiation (PAR) by 30% and 51% in AF and AF+, respectively, during the wheat cycle, together with a marked reduction of wind speed compared to controls (–85% in AF and -99% in AF+). A significant buffer effect was also highlighted for air temperature, averagely +1.7 °C during the night and -3.2 °C during the daytime under the moderate shading of AF. The positive effect of trees on soil water conservation increased with the intensity of shading, particularly during the critical wheat stage of grain filling, with benefits on wheat root mycorrhization, and NH4+ and NO3- abundance in the arable layer. Despite some of the environmental modifications being favorable for the understorey wheat, these were not translated into yield improvements, suggesting that the severe shading associated with the small inter-row and evergreen trees has a prevailing effect, that requires to be managed through appropriate tree pruning.