Indoor saffron farming systems under controlled conditions are required to meet the high demand for this valuable crop. The aim of the present study was to determine the flowering, growth, and yield responses of saffron grown using nutrient solutions with different electrical conductivity (EC) levels (0.7, 1.4, and 2.1 dS m−1). Sprouted saffron corms were cultured for 24 weeks under a volcanic rock-based aerated continuous immersion system. Vegetative growth and leaf gas exchange, but not flowering, were affected significantly by EC levels. The optimal EC in a balanced nutrient solution was 0.7 dS m−1, at which level the highest plant height, leaf area, biomass, photosynthetic rate, number of daughter corms, and percentage of corms ≥ 25 mm were recorded. An EC level of 2.1 dS m−1 decreased the photosynthetic rate, stomatal conductance, and transpiration rate of saffron but increased biochemical stress marker levels and elevated various antioxidant defense enzyme levels significantly in saffron leaves, possibly reflecting a defense response to the cellular damage provoked by the higher EC level. In terms of nutrient solution EC, 0.7 dS m−1 was optimal in saffron, whereas 2.1 dS m−1 caused oxidative stress that led to reduced growth and daughter corm production.