Imported mineral phosphate and fossil energy-intensive nitrogen fertilisers cause major detrimental impacts on the environment, whilst nutrient-rich side-streams/organic waste remain under-utilised. By optimising usage of bio-based fertilisers (BBF) from side-streams, ensuring their safety, building evidence-based trust in their usage and developing legislative framework for their use, it will be possible to reduce dependence upon mineral/fossil fertilisers, benefiting the environment and the EU’s economy. LEX4BIO aims to achieve this by collecting and processing regional nutrient stock, flow, surplus and deficiency data, and reviewing and assessing the required technological solutions. Furthermore, socioeconomic benefits and limitations to increase substitution of mineral fertiliser for BBFs will be analysed. A key result of LEX4BIO will be a universal, science-based toolkit for optimising the use of BBFs in agriculture and to assess their environmental impact in terms of non-renewable energy use, greenhouse gas emissions and other LCA impact categories. LEX4BIO provides for the first time connection between production technologies of BBFs and regional requirements for the safe use of BBFs. The large variation between EU regions in nutrient flows and regional requirements for fertilisers will be estimated by harmonised methods to produce the knowledge basis needed to set up feasible ways to redirect the nutrient flows where needed. This will be followed by classifying the best available technologies for producing regionally tailored BBFs to secure high agricultural productivity, as well as environmental protection, food safety and human health. In LEX4BIO, the knowledge basis and recommendations will be gathered and processed together with stakeholders across Europe, providing best solutions for decreasing the dependency on imported fertilisers, closing the nutrient cycles and improving sustainability of European farming systems.