Agricultural researchers widely recognise the importance of sustainable agricultural production systems and the need to develop appropriate methods to measure sustainability. The principal purpose of this paper is to evaluate the financial and environmental aspects of sustainability of Organic, Integrated and Conventional Farming Systems (OFS, IFS, and CFS, respectively) at farm and more detailed spatial scales. This is achieved applying an integrated economic-environmental accounting framework to three case study farms in Tuscany including different farming systems and different spatial scales. The environmental performances of the FS were measured through the application of an Environmental Accounting Information Systems (EAIS) at field, site and farm level. The EAIS indicators were then integrated with (1) a set of financial indicators to evaluate the economic and environmental trade-offs between different FS and (2) with information on the regional and site-specific soil and climate conditions to study the impact of different pedo-climates on the environmental performances of the FS. The gross margins of steady-state OFS were found to be higher than the corresponding CFS gross margins. OFS perform better than I/CFS with respect to nitrogen losses, pesticide impact, herbaceous plant biodiversity and most of the other environmental indicators. However, on hilly soils, erosion revealed to be higher in OFS than in CFS. The pesticide and the nitrogen indicators showed, for this example, that the environmental impact due to integrated and conventional farming practices is similar. Regional pedoclimatic factors resulted to have a considerable impact on nutrient losses, soil erosion, pesticide impact and herbaceous plant biodiversity, site-specific factors on nutrient losses and soil erosion. Conclusions are drawn on the possible practical applications of the method for environmental measures in the agricultural sector.