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The industrial production of conifer seedlings in nurseries uses large amounts of fertilizers to ensure their proper growth and accurate nutrient status. However, inorganic nitrogen fertilization leads to nitrate leaching, which has negative environmental consequences. An alternative solution could be the use of controlled-release fertilizers that supply nutrients over longer periods and hence have a lower environmental impact. This study analysed the performance of a novel arginine–iron–hexametaphosphate complex on Scots pine (Pinus sylvestris) seedlings. The complex was characterized using a wide range of analytical tools, indicating that it is a precipitated complex rather than a crystalline compound. Plant growth on arginine–iron–hexametaphosphate was comparable to a commercial inorganic nitrogen controlled-release fertilizer but with significantly lower nitrate leaching. A nitrogen budget of seedlings and growth substrate showed that seedlings had acquired nitrogen in excess of the amount of nitrogen present at the start of the experiment, and this excess nitrogen was smaller in seedlings grown on the inorganic fertilizer. Measurements of acetylene reduction in seedlings indicated low but measurable rates of nitrogen fixation, potentially contributing to the excess nitrogen. Together, the results showed that the arginine–iron–hexametaphosphate complex is a good alternative to commonly used fertilizers and can contribute to sustainable seedling production.