Improving seedling quality is a key objective in commercial horticulture, as it directly influences crop establishment, productivity, and performance in the field. Mycopriming, the application of bioactive fungal compounds to seeds, represents a sustainable strategy to enhance early plant development. In this study, we investigated the effects of seed priming with extracts derived from the mycelium and culture filtrates of endophytic fungi in Solanum lycopersicum seedlings under nursery conditions. Greenhouse trials were conducted to assess germination dynamics, root and shoot development, and physiological traits, including chlorophyll content, the flavonol index, and the anthocyanin index. Although germination percentage and shoot-related traits did not show significant variation compared to the control, both types of fungal extracts consistently enhanced root development across experiments. The culture filtrate extract increased root length by 33% (p < 0.05) and root dry weight by 32% (p < 0.05) compared to the control, while the mycelial extract increased root length by 25% (p < 0.05) and root dry weight by 22% (p < 0.05) compared to the control. This stimulation of root growth is particularly relevant for improving water and nutrient uptake capacity, which are critical for early seedling vigor and transplant success. These results demonstrate the potential of fungal metabolite-based seed treatments as a practical and efficient tool to improve the physiological quality of nursery-grown tomato seedlings. The use of naturally derived fungal extracts provides an environmentally friendly alternative to synthetic growth regulators, aligning with the principles of sustainable agriculture. Overall, mycopriming with fungal endophyte extracts emerges as a promising technique to support early-stage development and seedling vigor in tomato production, especially in nursery systems focused on delivering high-quality transplants.