Consumers are increasingly interested in knowing the environmental impacts of foods. In addition, producers are interested in receiving recommendations to reduce their impacts. This faces two major challenges: (1) certain systems are not widely studied and (2) not all production stages are included in system boundaries (e.g. only the agricultural stage or the supply chain). Life Cycle Assessment was applied to a specific small-scale and low-input organic apple value chain. The system boundaries included the cultivation, processing and distribution. All transport and waste management were considered. The main contributors to environmental impacts are: cultivation, juice and applesauce production, retail and consumption. Compared to literature, cultivation is efficient. Processing and retail are respectively influenced by the use of glass packaging, the cold storage of fresh apples and the transport to stores. Consumption was influenced by the management of apple waste and the consumer trip. Literature survey and results confirm that the system was not represented in the literature and provides new insights into the entire value chain, as well as new proxy LCIs. Similar specific studies should be repeated in the future to cover the variability. It is an essential step towards applying the environmental footprint fairly to alternative systems.