Peat, a non-sustainable resource, is still predominately used in forest nurseries. Coconut coir might provide an alternative, renewable, and reliable growing media but few studies have evaluated this media type in forest nurseries. We assessed the influence of pure coir, in combination with various fertilization regimes, on the growth and physiology of three ecologically diverse Quercus species seedlings (Q. robur, Q. pubescens, and Q. ilex) during nursery cultivation. Seedlings were grown using peat and pure coir in combination with three fertilization treatments (standard, K-enriched, and P-enriched). Data were collected for: (1) growth and physiological traits; (2) detailed above- and below-ground morphological traits by destructive analysis; and (3) NPK content in leaves, shoot and roots, and in the growing media, following cultivation. Peat and coir in combination with the various fertilization treatments affected above- and below-ground morphology and, to a lesser extent, the physiological traits of Quercus seedlings. Large effects of the substrate occurred for most morphological variables, with peat being more effective than coir in all studied species. Fertilization also produced significant differences. The effect of K-enriched fertilization on plant growth was clear across the three species and the two growing media. P-enriched fertilization in peat was the only combination that promoted a higher amount of this element in the tissues at the end of cultivation. Despite their smaller size, seedlings produced in coir were compatible with standard Quercus forest stocktype size, and showed a proportionally higher root system development and fibrosity. Our results suggest that coir can be used as an alternative substrate to grow Quercus species seedlings, and that fertilization can offset coir deficiencies in chemical properties. As several functional traits drive planting performance under varying environmental conditions. according to the Target Plant Concept, coir might thus serve as an acceptable material for seedling cultivation in some cases.