When trying to optimize the sustainability performance of farms and farming systems, a consideration of trade-offs and synergies between different themes and dimensions is required. The aim of this paper is to perform a systematic analysis of trade-offs and synergies across all dimensions and themes. To achieve this aim we used the Sustainability Monitoring and Assessment Routine (SMART)-Farm Tool which operationalizes the Sustainability Assessment of Food and Agriculture Systems (SAFA) Guidelines by defining science-based indicator sets and assessment procedures. It identifies the degree of goal achievement with respect to the 58 themes defined in the SAFA Guidelines using an impact matrix that defines 327 indicators and 1769 relations between sustainability themes and indicators. We illustrate how the SMART-Farm Tool can be successfully applied to assess the sustainability performance of farms of different types and in different geographic regions. Our analysis revealed important synergies between themes within a sustainability dimension and across dimensions. We found major trade-offs within the environmental dimension and between the environmental and economic dimension. The trade-offs within the environmental dimension were even larger than the trade-offs with other dimensions. The study also underlines the importance of the governance dimension with regard to achieving a good level of performance in the other dimensions.