This VEGINECO manual is one of a series of publications resulting from the VEGINECO project. VEGINECO specialises in producing tested and improved multi-objective farming methods for key farming practices – e.g. crop rotation, fertilisation and crop protection – to facilitate the integration of potentially conflicting objectives like economy and ecology. This report consists of two parts. The first part describes the prototyping methodology and how it was used in the VEGINECO project (Chapters 2 - 5). The second part describes the methodology for developing crop rotation strategies with examples of its application under different conditions in Europe (Chapter 6 - 11)