LCA methodology provides the best framework to evaluate environmental impacts in agriculture systems. However, the interpretation of LCA results, in particular when the objective was to compare different production systems, could be affected by the selection of the functional unit (FU). That is why an accurate definition of the FU, in agreement with the function considered for the systems analysed, is essential. In this work, the organic production at small scale of blueberry, raspberry, blackberry and cape gooseberry in North Spain has been analysed following LCA methodology. Although a different distribution of environmental loads was obtained for each crop, in all cases, the main contributions to most of the considered environmental categories were electric and fertiliser consumptions. The different production systems have been compared on the basis of the environmental impacts associated considering different FUs, i.e. based on fruit mass, cultivated area, farm-gate price and nutritional quality of fruits. Carbon footprints (CF) have been also calculated. It was observed that the order of the crops with respect to their environmental performances was the same for the blueberry and raspberry crops (with the lowest and the highest CF, respectively), independently of the selected FU, whereas the order of the blackberry and cape gooseberry crops was interchanged, depending on the FU used. This work supports the need of being aware of the final objective of the orchards when choosing the FU (i.e. producing fruits, cultivating an area, economic benefits or nourishing people), so that valid conclusions can be achieved from the environmental comparison, even for different agricultural products.