Agriculture plays a central role in achieving most Sustainable Development Goals (SDGs). Sustainable intensification (SI) of agriculture has been proposed as a promising concept for safeguarding global food security, while simultaneously protecting the environment and promoting good quality of life. However, SI often leads to context-specific sustainability trade-offs. Operationalising SI thus needs to be supported by transparent sustainability assessments. In this article, we propose a general systematic approach to developing context-specific frameworks for integrated sustainability assessment of agricultural intensity change. Firstly, we specify a comprehensive system representation for analysing how changes in agricultural intensity lead to a multitude of sustainability outcomes affecting different societal groups across geographical scales. We then introduce a procedure for identifying the attributes that are relevant for assessment within particular contexts, and respective indicator metrics. Finally, we illustrate the proposed approach by developing an assessment framework for evaluating a wide range of intensification pathways in Europe. The application of the approach revealed processes and effects that are relevant for the European context but are rarely considered in SI assessments. These include farmers’ health, workers’ living conditions, cultural heritage and sense of place of rural communities, animal welfare, impacts on sectors not directly related to agriculture (e.g., tourism), shrinking and ageing of rural population and consumers’ health. The proposed approach addresses important gaps in SI assessments, and thus represents an important step forward in defining transparent procedures for sustainability assessments that can stimulate an informed debate about the operationalisation of SI and its contribution towards achieving SDGs.