In recent years, farmers and policymakers have faced ample challenges and have struggled to support the sustainability of the agricultural sector. Sustainable agriculture encompasses multiple concepts, and its performance produces extensive debate about data requirements, appropriate indicators, evaluation methods, and tools. Under the European Union (EU) financed project FLINT (Farm Level Indicators for New Topics in policy evaluation), detailed data have been collected at the farm level to provide broader coverage of sustainability indicators on a wide range of relevant topics to facilitate the assessment of sustainability performance. The approach has been applied in a pilot network of representative farms at the EU level, considering the heterogeneity of the EU farming sector to provide data infrastructure with up to date information for sustainability indicators. This study aims to assess sustainability performance at the farm level in Greece. Representative and dominant agricultural systems, such as permanent crops, olive trees, arable crops, and livestock (sheep) farms, comprise the Greek sample. It uses the analytical hierarchy process (AHP) methodology and attempts to gain insights into the sustainability performance of agricultural systems. The outcome of the sustainability assessment reveals knowledge and develops support for strategic farm choices in order to support both farmers and policymakers towards more sustainable development plans. The results indicate that three typical Mediterranean farming systems, namely permanent crops, olive trees, and extensive livestock systems (sheep farms), are more sustainable in contrast to intensive and arable crop farms.