The UNISECO project aims to provide recommendations on how the sustainability of agro-ecological farming systems (AEFS) in Europe can be promoted. These recommendations build also upon model-based upscaling to territorial level of case-study based results on various AEFS throughout the partner countries. This deliverable in detail describes the models to do this upscaling, starting with the general context, the description of the conceptual aspects of the mass- and nutrient-flow modelling as used in UNISECO, and then the detailed description of the two biophysical models employed for this.