In the absence of mineral fertiliser, animal manure may be the only nutrient resource available to smallholder farmers in Africa, and manure is often the main input of C to the soil when crop residues are removed from the fields. Assessments of C and nutrient balances and cycling within agroecosystems or of greenhouse gas emissions often assume average C and nutrient mass fractions in manure, disregarding the impact that manure storage may have on C and nutrient losses from the system. To quantify such losses, in order to refine our models of C and nutrient cycling in smallholder (crop-livestock) farming systems, an experiment was conducted reproducing farmers' practices: heaps vs. pits of a mix of cattle manure and maize stover (2:3 v/v) stored in the open air during 6 months. Heaps stored under a simple roof were also evaluated as an affordable improvement of the storage conditions. The results were used to derive empirical models and graphs for the estimation of C and nutrient losses. Heaps and pits were turned every month, weighed, and sampled to determine organic matter, total and mineral N, P and K mass fractions. Soils beneath heaps/pits were sampled to measure mineral N to a depth of 1 m, and leaching tube tests in the laboratory were used to estimate P leaching from manure. After 6 months, ca. 70% remained of the initial dry mass of manure stored in pits, but only half of or less of the manure stored in heaps. The stored manure lost 45% of its C in the open air and 69% under roof. The efficiencies of nutrient retention during storage varied between 24-38% for total N, 34-38% for P and 18-34% for K, with the heaps under a roof having greater efficiencies of retention of N and K. Laboratory tests indicated that up to 25% of the P contained in fresh manure could be lost by leaching. Results suggest that reducing the period of storage by, for example, more frequent application and incorporation of manure into the soil may have a larger impact on retaining C and nutrient within the farm system than improving storage conditions.