The role of livestock in maintaining landscapes, their role in delivering proteins and other nutrients for human diets, but also the downsides of livestock production contributing to environmental degradation and human health problems, are topics of considerable debate. To assess the risk and benefits arising from livestock production, transparent and robust indicators are required, such as those offered by life cycle assessment. A central question in such approaches is how environmental burden is allocated to edible and non-edible livestock products and to manure that is re-used for agricultural production. For giving incentives for sustainable use of manure, it should be considered as co-product as long as it is not applied in excess of crop nutrient needs, and as waste otherwise. This paper proposes a theoretical and pragmatic approaches to allocate burden to manure and other livestock products based on the value for crop production it delivers to the farmer, on the example of value of nutrients. We illustrate and discuss the method with two case studies.