Livestock production is confronted with significant challenges across all dimensions of sustainability. There is an urgent need to identify sustainable livestock systems that are environmentally friendly, economically viable for farmers, and socially acceptable. To this end, diversity assessments and data-driven indicator-based sustainability assessments can be helpful tools. These two mutually reinforcing approaches each have their own dilemmas and strengths; however, their combination is not straightforward. In this paper, we propose a method that simultaneously assesses the diversity and sustainability of production systems within one agricultural sector, without compromising either aspect, while overcoming the dilemmas of diversity and sustainability assessments. We test our method on the Walloon dairy and beef sectors (Belgium) and base our assessment on data from the European Farm Accountancy Data Network (FADN). We apply relevant classification criteria to the sample farms to group them into production systems. The core data was complemented with calculated environmental indicators to perform a comprehensive sustainability assessment, including structural, socio-economic, and environmental indicators. Our results confirm the importance of complementing sustainability assessments with diversity assessments. Our case study results show that a diversity of livestock systems coexist and that it is possible to overcome trade-offs between economic and environmental performances. Extensive grass-based systems present the best combination of economic and environmental results, which highlights the importance of preserving grassland resources at the regional level. The proposed method proves effective to improve the relevance of FADN data and supports the ongoing call to transform the FADN into a more comprehensive database that satisfactorily covers all dimensions of sustainability.