The adaptation of semi-arid crops to climate changes is theoretically possible in agroforestry systems (AFS), provided that the trees exert little competition, or even increase the land equivalent ratio (LER). However, the measurement of LER requires sole crop plots which are usually not available in AFS. We designed a geostatistical method to estimate the distance of influence of trees on crops and selected sole crop plots at even higher distances, in order to compute LER. We monitored microclimate, net primary productivity (NPP), CO2 and H2O fluxes in a semi-arid agro-silvo-pastoral system (Niakhar, Senegal), dominated by the multipurpose Faidherbia albida (FA) tree. Undercrops were mainly millet and peanut, under annual rotation. Just before harvest, we scanned a ca. 1 ha millet plot under FA with UAV photogrammetry (drone) in RGB, thermal infrared and multispectral bands. At harvest, we collected 12 subplots, distributed either below the crown of FA, or at 2.5 x the crown radius (CR), or at 5 CR. We separated all organs. The whole millet root system (0-200 cm) was sampled also in 2 m trenches. Whole plot harvest allowed extrapolating yield from subplots, through UAV images. Millet yield per unit ground area was about 3 times higher below FA. The geostatistical method indicated that NDVI was not affected by the FA trees at 5 times the crown radius. LER of millet was computed 1.4, confirming the positive effect FA at distances up to 18 m. The “Faidherbia-Flux” observatory is open for collaboration.