ABSTRACT.- Perennial fruit production at the commercial scale, such as citrus fruits, begins with seedling production in a nursery. This stage lasts several months and involves different phases and the use of substrates and infrastructure. As the seedling does not produce fruit but does consume inputs, studying the environmental impacts associated with this stage becomes relevant, especially to understand its contribution to the total impact of the crop cycle. Despite the global relevance of fruit tree seedlings production, LCA studies in the literature focus on horticultural crop nurseries, and those on perennial tree nurseries do not consider both substrate and structures in the analysis, which is key for this type of crop since the main production system is soilless production in greenhouses. Thus, the main goal of this study is to quantify the environmental impacts related to the production of citrus fruit tree seedlings using LCA, analyse the main production system applied nowadays, and study its relevance with respect to the crop cycle. To this end, a certified Uruguayan citrus nursery was analysed, from which primary data was obtained. As well, methodological issues concerning water consumption and modelling emissions from input applications in soilless greenhouse systems are tackled. Results show that the main hotspots of the nursery stage are infrastructure production and peat transportation, which highlights the relevance of their inclusion when modelling the system. Extending the lifespan of the galvanised steel structures and decreasing substrate transport distances are shown to be effective measures to reduce environmental impacts. The contribution of the nursery stage to the citrus production cycle is negligible for almost all the impact categories assessed except cancer human toxicity, as it accounts for 0-3.6% of the impacts depending on the impact category. Great differences (from 10 to 400 times higher results on average) are observed when comparing the results with those from commercial databases, as they consider open-field nurseries where seedlings are grown in the soil. The need to develop harmonised methods to model water consumption and fertiliser and pesticide emissions for soilless crops in greenhouses arises. The present study presents a complete quantification of the environmental impacts of the main production system of citrus fruit tree seedlings and provides scientific and quantitative evidence of its contribution to the production cycle, helping decision-makers understand where efforts should be focused to achieve a more sustainable fruticulture. © 2024 The Authors