<p>Mycorrhizal associations play a crucial role in afforestation efforts, as they enhance the acquisition of nutrients and water, thereby supporting seedling establishment. However, the influence of nitrogen (N) forms in the soil, particularly the organic N, on the formation of mycorrhizal associations and their subsequent effects on seedling morpho-physiology remains poorly understood. In this study, we examine the mycorrhizal colonization, along with morpho-physiological and functional traits, in <i>Pinus cooperi</i> seedlings following fertilization with organic N in controlled nursery conditions. A factorial experiment was performed with <i>Pinus cooperi</i> C. E. Blanco seedlings using two N sources: organic N (amino acids) and inorganic N (NH₄NO₃) and two N doses: low and high (60 vs 200 mg N seedling⁻¹). Seedlings were inoculated with a mixture of native fungi, but the phylogenetic analysis showed that <i>Suillus placidus</i> (Bonord.) Singer was the only species colonizing roots. Organic N promoted similar morphology and nutritional status as inorganic N, though at a low N rate, it improved root growth and mycorrhizal colonization. High N fertilization improved seedling growth and nutritional status but reduced mycorrhizal colonization. Mycorrhizal colonization improved needle P concentration, delayed plant desiccation, and reduced root cellular damage when seedlings were subjected to desiccation, though it decreased plant growth and needle N concentration. We conclude that organic N fertilization improves mycorrhization of <i>P. cooperi</i> with <i>S. placidus</i>, but the fertilization dose should be adjusted to meet species-specific requirements in order to optimize plant quality and promote afforestation success.</p>