A variety of indicator-based methods have been developed for the sustainability assessment of farming systems (FSs). However, many of them lack holisticity, focus on a specific agricultural sector/product, and do not provide aggregated results to better support decision-making process. The goal of this study was, for the first time, to assess, in a holistic manner, the sustainability performance of different FSs in southeastern Cyprus. The methodological framework involved three major steps. First, the sustainability context was set, and a list of 41 environmental, social, and economic indicators was created. The indicators were then calculated using data from 324 farms. Second, six FSs were identified using multivariate analysis. Finally, the sustainability of FSs was assessed by combining numerical (construction of four composite sustainability indices) and visual (presentation of indicator scores and values with graphs and tables) integration approaches. While the indices provided the “big picture”, visual integration revealed the areas where policy interventions are needed. The analysis showed that sustainable agricultural practices are already used by some farmers in the area. The results could be used for benchmarking purposes and to aid decision-making process in Cyprus but might also be useful for other Mediterranean regions with similar agro-ecological conditions.