Agriculture in semi-arid Burkina Faso is dominated by mixed crop-livestock smallholder farms with limited investment capacity in production factors, such as improved seeds, fertilizer and equipment. Hence, to make a living, farmers try to make the best use of available resources based on principles of agro-ecology, including crop diversity and nutrient and biomass recycling. We investigated farm-level management of resources (soil, crops and livestock) through time to assess whether the current management options were able to sustain crop and livestock production and fulfil household food requirements. We ran a one-year detailed farm monitoring campaign in collaboration with 22 volunteer farmers representing the diversity of the farming system in our study area. We quantified inputs and outputs in the cropping system (177 fields) for one rainy season. In addition, the weekly dynamics of crop residues left on field were quantified. Moreover, inflow and outflow of resources at farm level were quantified weekly. The cropping system was characterized by a negative nitrogen balance of about 12 kg N/ha/year, with market-oriented farms and large livestock owners having the most negative balance. Legumes grown (sole and intercropping) contributed to alleviate the nitrogen depletion by adding 15 kg N/ha/year to the nitrogen inputs through atmospheric fixation. However, cereal-legume intercropping did not significantly reduce the nitrogen deficit in comparison to sole cereal cropping mainly because of the small proportion of legumes (8%) in intercropped fields. Livestock grazed crop residues left on the soil (739 kg dry matter/ha on average) at a rate of 26 - 76 kg/ha/week, thus strongly reducing the potential for mulching in the region. Livestock protein requirements were rarely met from farm-produced feed with average feed gaps ranging between 40% and 89% of the daily requirements for small and large herd keepers respectively. Large livestock (cattle) owners relied on trans