Afforestation in semi-arid regions can potentially enhance the global carbon sink by increasing the terrestrial biomass. However, the survival of planted forests under such extreme environmental conditions is not guaranteed a priori, and critically depends on the surface–atmosphere exchange of energy. We investigate the pine forest Yatir in Israel, an example of a man-made semi-arid ecosystem, by means of large-eddy simulations. We focus on the interaction between surface–atmosphere exchange and secondary circulations that couple the isolated forest to the surrounding shrubland. The large-eddy simulations feature a grid resolution that resolves the forest canopy in several layers, and are initialized by satellite data and Doppler lidar, eddy-covariance and radiosonde measurements. We perform three large-eddy simulations with different geostrophic wind speeds to investigate the influence of those wind speeds on the surface–atmosphere exchange. We reproduce the measured mean updrafts above the forest and mean downdrafts above the shrubland, which increase in strength with decreasing geostrophic wind speed. The largest updrafts emerge above the older, denser part of the forest, triggering secondary circulations. The spatial extent of these circulations does not cover the entire forest area, although we observe a reduced aerodynamic resistance in the regions of updraft. Our simulations indicate that the enhanced surface–atmosphere exchange of the Yatir forest is not sufficient to compensate for the increased net radiation, due to the lower albedo of the forest with respect to the surroundings, resulting in higher air temperatures inside the forest. However, the difference between the forest and shrubland temperatures decreases with increasing geostrophic wind speed due to reduction in the aerodynamic resistance.