The MilKey project aims at assessing the environmental, economic, and social sustainability of European dairy production systems, and at identifying ‘win-win’ farming practices for sustainable and greenhouse gas (GHG) optimised milk production. In this context, a holistic model was developed to evaluate the sustainability of specialised dairy farms and was entitled DEXi-Dairy. This model has the potential of aiding the identification of GHG and nitrogen (N) emission mitigation options and assessing their effects across multiple sustainability aspects. DEXi-Dairy covers the three sustainability pillars, i.e., environmental, economic, and social. Based on the ‘DEX’ multi-criteria methodology, the model is detailed under the form of a tree structure represented by four main hierarchical layers, i.e., branches, principles, criteria, and indicators. DEXi-Dairy was built following a participatory and interdisciplinary approach by MilKey project partners. It was then tested on three case study farms from Ireland, France, and Germany, respectively, using data from 2020. The DEXi-Dairy indicator handbook describes the sustainability tree and selected indicators to assess dairy production systems over a production year. Overall, this document can be used as a basis to replicate and expand the sustainability assessment framework developed as part of the MilKey project.