Plant factories with precise control systems create a stable microenvironment, making them essential for cultivating stronger, more uniform seedlings needed for high-quality production. Among the various factors influencing seedling quality, planting density plays a critical role as a key management practice. To explore this relationship, the combined effects of cultivation facilities and planting densities on tomato (Solanum lycopersicum L.) seedlings were investigated in this study. Two facilities were compared: a plant factory with artificial light (PFAL) and a glasshouse with natural light (GHNL). The results revealed that the specific leaf area, health index, ratio of dry weight to fresh weight, and radiation use efficiency (RUE) were predominantly affected by planting density, whereas plant height, leaf area, chlorophyll content, and epicotyl and hypocotyl lengths were mainly influenced by the cultivation facilities. The stem diameter was minimally affected by these conditions. The epicotyl and hypocotyl lengths were significantly greater in the GHNL, while the stem diameter remained unchanged. Seedlings grown in the GHNL had a higher fresh weight, but similar dry weight compared with those grown in the PFAL, with the lowest leaf-to-stem weight ratio observed in the GHNL for both fresh and dry weights. Among treatments, natural light with low planting density (NL, 80 seedlings per tray) produced the highest dry weight, whereas artificial light with high planting density (AH, 240 seedlings per tray) resulted in the lowest. Both the health index and the ratio of dry weight to fresh weight were enhanced with low planting density. The PFAL significantly increased the chlorophyll and carotenoid levels. Furthermore, the RUE of seedlings with high planting density was significantly greater than seedlings with low planting density. The combination of a higher planting density and the PFAL appears to offer certain benefits for seedling production, including graft suitability and production costs.