Using greenhouse tomato ( Solanum lycopersicum ) as a model system to produce pharmaceutical proteins, electrical conductivity (EC) of hydroponic nutrient solution was examined as a possible factor that affects the protein concentration in fruit. Transgenic tomato plants, expressing F1-V protein, a plant-made candidate subunit vaccine against plague ( Yersinia pestis ), were grown hydroponically at high (5.4 dS·m ⁻¹ ) or conventional EC [2.7 dS·m ⁻¹ (control)] with a high-wire system in a temperature-controlled greenhouse. There was no significant difference in plant growth and development including final shoot dry weight (DW), leaf area, stem elongation rate, or leaf development rate between high EC and control. Net photosynthetic rate, transpiration rate, and stomatal conductance ( g _S ) of leaves were also not significantly different between EC treatments. For both EC treatments, immature green fruit accumulated DW at a similar rate, but dynamics observed in fruit total soluble protein (TSP) and F1-V during the fruit growth were different between the two ECs. Fruit TSP concentration per unit DW decreased while TSP content per whole fruit increased as fruit grew, regardless of EC. However, TSPs were significantly lower in high EC than in control. Fruit F1-V concentration per unit DW and F1-V content per whole fruit were also lower in high EC than in control. Our results found that increasing EC of nutrient solution decreased TSP including the vaccine protein in fruit, suggesting that adjusting nutrient solution EC at an appropriate level is necessary to avoid salinity stress in this transgenic tomato.