Agro-silvo-pastoralism is a highly representative Land Use in Africa, often presented as a strategical option for ecological intensification of cropping systems towards food security and sovereignty. We set up a new long-term observatory (“Faidherbia-Flux”) to monitor and model microclimate, energy and C balance in Niakhar (central Senegal, rainfall ~ 500 mm), dominated by the multipurpose tree Faidherbia albida (12.5 m high; 7 tree ha-1; 5% canopy cover). Faidherbia is an attractive agroforestry tree species in order to partition fluxes, given that it is on leaf during the dry season (October-June) and defoliated during the wet season, just when crops take over. Pearl-millet and groundnut crops were conducted during the wet season, following annual rotation in a complex mixed mosaic of ca. 1 ha fields. Early 2018, we installed an eddy-covariance (EC) tower above the whole mosaic (EC1: 20 m high). A second EC system was displayed above the crop (EC2: 4.5 m if pearl-millet, 2.5 m if groundnut) in order to partition ecosystem EC fluxes between tree layer and crop+soil layers. Sap-flow was monitored from April 2019 onwards in 5 faidherbia trees (37 sensors). The ecosystem displayed moderate but significant daily CO2 and H2O fluxes during the dry season, when faidherbia (low canopy cover) was in leaf and the soil was evaporating. At the onset of the rainy season, the soil bursted a large amount of CO2. Just after the growth of pearl-millet in 2018, CO2 uptake by photosynthesis increased dramatically. However, this was largely compensated by high ecosystem respiration. Surprisingly in 2019, although the crop was turned to groundnut, the fluxes behaved pretty much the same as with pearl millet in 2018: comparing annual balances between 2018 and 2019 we obtained [454, 513] for rainfall (P: mm yr-1), [3500, 3486] for potential evapotranspiration (ETo: mm yr-1), [0.13, 0.15] for P/ETo, [470, 497] for actual evapotranspiration (E: mm yr-1), [2809, 2785] for net radiation (Rn: