Success in long-term agricultural production in resource-poor farming systems relies on the efficiency with which nutrients are conserved and recycled. Each transfer of nutrients across the farming system provides a risk of inefficiency, and how much is lost at each step depends on the type of farming system, its management practices and site conditions. The aim of this review was to identify critical steps where efficiency of nitrogen (N) cycling through livestock in smallholder crop-livestock farming systems could be increased, with special emphasis on Africa. Farming systems were conceptualised in four sub-systems through which nutrient transfer takes place: (1) livestock: animals partition dietary intake into growth and milk production, faeces and urine; (2) manure collection and handling: housing and management determine what proportion of the animal excreta may be collected; (3) manure storage: manure can be composted with or without addition of plant materials and (4) soil and crop conversion: a proportion of the N in organic materials applied to soil becomes available, part of which is taken up by plants, of which a further proportion is partitioned into grain N. An exhaustive literature review showed that partial efficiencies have been much more commonly calculated for the first and last steps than for manure handling and storage. Partial N cycling efficiencies were calculated for every sub-system as the ratio of nutrient output to nutrient input. Estimates of partial N cycling efficiency (NCE) for each sub-system ranged from 46 to 121% (livestock), 6 to 99% (manure handling), 30 to 87% (manure storage) and 3 to 76% (soil and crop conversion). Overall N cycling efficiency is the product of the partial efficiencies at each of the steps through which N passes. Direct application of plant materials to soil results in more efficient cycling of N, with fewer losses than from materials fed to livestock. However, livestock provide many other benefits highly valued by farmers, and animal manures can contain large amounts of available N, which increases the immediate crop response. Manures also can contribute to increase (or at least maintain) the soil organic C pool but more quantitative information is needed to assess the actual benefits. Making most efficient use of animal manures depends critically on improving manure handling and storage, and on synchrony of mineralisation with crop uptake. Measures to improve manure handling and storage are generally easier to design and implement than measures to improve crop recovery of N, and should receive much greater attention if overall system NCE is to be improved.