Improving the eco-efficiency of food systems is one of the major global challenges faced by the modern world. Short food supply chains (SFSCs) are commonly regarded to be less harmful to the environment, among various reasons, due to their organizational distribution and thus the shortened physical distance between primary producers and final consumers. In this paper, we empirically test this hypothesis, by assessing and comparing the environmental impacts of short and long food supply chains. Based on the Life Cycle Assessment (LCA) approach, we calculate eco-efficiency indicators for nine types of food distribution chains. The analysis is performed on a sample of 428 short and long food supply chains from six European countries. Our results indicate that, on average, long food supply chains may generate less negative environmental impacts than short chains (in terms of fossil fuel energy consumption, pollution, and GHG emissions) per kg of a given product. The values of eco-efficiency indicators display a large variability across analyzed chains, and especially across different types of SFSCs. The analysis shows that the environmental impacts of the food distribution process are not only determined by the geographical distance between producer and consumer, but depend on numerous factors, including the supply chain infrastructure.