Agricultural by-products, that is primary residue, industrial by-products and animal manure, are an important source of nutrients and carbon for maintaining soil quality and crop production but can also be valorised through treatment pathways such as fermentation, incineration or a combination of these called bio-refinery. Here, we provide an overview of opportunity to reduce environmental impact of valorising agricultural by-products. We estimate the available by-products in Northwestern Europe as a case study and the maximum and realistic greenhouse gas reduction potentials. Availability, collectability, the original use and environmental impact including land use changes, soil carbon sequestration and pollution swapping are discussed as critical factors when valorising agricultural by-products.