Highlights • First LES simulations of wind dynamics and spore dispersal in agroforestry systems. • Two levels of mixing-layer-type coherent motions are observed, at crop and tree tops. • Trees accentuate fine-spore dispersal while enhance deposition of coarse spores. • A wind velocity profile parameterization is proposed for agroforestry systems. Abstract Agroforestry systems associating trees with crops are gaining a growing interest due to their environmental benefits in a context of climate change and biodiversity loss. Still, the impact of trees on the wind dynamics within agroforestry systems remains poorly understood despite the key role played by the wind in energy and mass exchanges, including disease and pest propagation. Here, we present the first detailed analysis of the wind dynamics over agroforestry systems, combining in situ measurements and instantaneous airflow simulations, with a numerical application on spore-like particle dispersion from an infection point source at crop top. Simulations reproduce remarkably well most characteristics of the turbulent wind flow within the agroforestry system. Simulations reveal the presence of two inflection points on the mean wind velocity profile, at crop and tree tops, both inducing the development of mixing-layer type eddies, controlling most of the turbulent exchanges within the agroforestry system. Relative to the local wind, the turbulence at the crop scale is more intense and intermittent in presence of trees. With increasing tree density, the turbulence at crop top becomes dominated by tree-scale motions developing at tree top. The presence of trees has a different impact on particle dispersion according to the particle size and the wind intensity. Trees accentuate the vertical and transversal dispersal of submicron spores while they enhance the short-range deposition of coarser spores on crops, the more as the wind is low, and thus limit the long-range dispersal of coarse spores. Finally, a simple parameterization of the mean wind velocity vertical profile is proposed for agroforestry systems, depending only on the foliage densities and heights of the tree and crop layers. This parameterization leads to an indication of the agroforestry system efficiency to limit spore propagation through an estimation of the Rouse number at crop top.