Eco-efficiency is commonly used as an indicator of sustainability since it expresses the efficiency with which natural resources are utilized to meet people’s needs. Agriculture relies heavily on these ecological resources and by-produces significant environmental burdens, shifting the interest of researchers and policymakers toward the promotion of ecological practices. However, limited evidence exists regarding eco-efficiency across various ecological approaches like low input, conservation, and organic farming. This paper contributes to the existing literature and provides insight into the eco-efficiency of Cretan olive farms managed under different ecological approaches. Olive oil production is vital for the socio-economic sustainability of Mediterranean agriculture, a significant element of the region’s culture, and the basis of the well-known “Mediterranean diet”; therefore, it is crucial to investigate eco-efficient management options for olive farmers. Data Envelopment Analysis (DEA) and a second-stage statistical analysis are employed to estimate the eco-efficiency of olive farms and investigate factors affecting it. Composite indicators for biodiversity, soil, and input management are incorporated in the eco-efficiency model. The results indicate that organic farms achieve the highest eco-efficiency scores, followed by other ecological approaches. Additionally, eco-efficiency seems to be explained by farmers’ dependency on subsidies, commitment to farming activity, and environmental awareness.