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Purpose: Agricultural production, which dominates the environmental impacts of the food sector, has specific characteristics that need to be considered in life cycle assessment (LCA) studies. Agricultural systems are open, difficult to manage and control, strongly depend on natural resources and their impacts are highly variable and influenced by soil, climate and farm management. A specific framework, efficient methods and tools are thus needed to adequately assess the environmental impacts of agricultural systems. Methods: We present the Swiss Agricultural Life Cycle Assessment (SALCA) concept and method, developed for a detailed and specific analysis of agricultural systems. It comprises rules for the definition of system boundaries, functional unit and allocation, emission models, a life cycle inventory (LCI) database, calculation tools, impact assessment methods and concepts for analysis, interpretation and communication. This paper focuses on emission models for gaseous N, nitrate leaching, P emissions to water, soil erosion, pesticides, heavy metals, emissions from animal production and impact assessment methods for soil quality and biodiversity. The models are calculated at the crop, field, animal group and farm levels and are integrated in a consistent and harmonised framework, which is ensured by exchanging intermediate results between models. Results and discussion: The SALCA concept has been applied in numerous LCA studies for crops and crop products, cropping systems, animal husbandry systems and animal products, food and feed products, farms and product groups, the agrifood sector and food systems. The SALCA methodology has also been a backbone of the LCI databases ecoinvent, AGRIBALYSE and the World Food LCA database. The strengths of SALCA lie in its comprehensiveness, specificity to agriculture, harmonisation, broad applicability, consistency, comparability, flexibility and modularity. The extensive data demand and the high complexity, however, limit the application of SALCA to experts. The geographical scope is limited to Central and Western Europe, with a special focus on Switzerland. However, due to the modular and flexible design, an adaptation to other contexts is feasible with reasonable effort. Conclusions: SALCA enables answering a wide range of research questions related to environmental assessment and is applicable to various goals and scopes. A further development would be the inclusion of the social and economic dimensions to perform a full sustainability analysis in the SALCAsustain framework.