Besides producing food for humanity’s nutrition, agriculture also fulfills other functions such as providing a livelihood for farmers and preserving an attractive and biodiverse landscape. These functions of agriculture were considered in a novel eco-efficiency assessment concept applied to Austrian farms within this study. The joint application of life cycle assessment (LCA) and data envelopment analysis (DEA) was used to evaluate Austrian farms’ eco-efficiency. Data from 47 farms from different farm types (crop production, milk production, beef production, and wine production) were used to implement the concept. Cumulative exergy demand (CExD), global warming potential (GWP), normalized eutrophication potential (EP), and aquatic ecotoxicity potential (AE) were included as environmental impacts in an LCA and were consequently used as input values for the DEA. Considering multiple functions of agriculture, the farm net income (FNI), the net food production of crude protein and human-edible energy, and High Nature Value farmland (HNVf) were selected as output variables for the DEA. Results show that the purchase of resources causes a substantial share of environmental impacts, highlighting the importance of efficient utilization of on-farm resources. The results further revealed the use of high amounts of human-edible energy and protein as animal feed to cause lower eco-efficiency scores of livestock keeping farms (i.e., milk production and beef production). Overall, the eco-efficiency of farms depends on the fulfillment of different functions of agriculture, and individual strategies for improvement could be identified.