Given the increasing complexity of the agro-food sector, the analysis of financial performance alone may not be sufficient to assess the economic sustainability of farmers. This paper presents a practical method to measure the performance of farm businesses by combining the Balanced Scorecard (BSC) theoretical framework and Importance–Performance Analysis (IPA). The proposed model of Business Performance Indicators (BPI) measurement allows identification and validation of the indicators that consistently measure the latent dimension of the BSC framework while allowing identification Buin of the BPI areas where farm businesses need to concentrate their efforts to assure economic sustainability. The method was applied to small ruminant farm businesses across Europe through visits and interviews. The case study application showed that the model could help measure the performance of small farms while allowing detection of the areas of fragility and intervention. The case study results showed that finance and internal business management were the most relevant farmers’ weaknesses, alongside low priority given to innovation. In conclusion, to prevent the potential long-term decline of the sector, the study provided evidence for policy changes to support the farmers’ innovation potential and a higher level of integration in the supply chain.