Soluble solids content (Brix) is one of the most important agronomic traits in tomatoes. High Brix tomatoes are usually produced by applying water stress, which results in a significant reduction in fruit yield. We have developed a hydroponic method that utilizes coral sand as a solid medium and ICT technology for nutrient management to produce high Brix tomatoes without severe yield loss. In this study, we analyzed the mechanism behind the increase in Brix. Transcriptome analysis showed that the expression of phosphorus deficiency-inducible genes was increased in the leaves of tomato plants grown on coral sand. Phosphate concentration was decreased in both the nutrient solution and leaves when plants were grown on the coral medium, suggesting that a weak level of phosphorus deficiency response may be associated with the increase in Brix. We then grew tomatoes hydroponically to determine a phosphate concentration that induced a similar level of phosphate deficiency response as the coral sand culture. We found that under the low phosphate condition, fruit Brix was increased even though fruit yield was reduced. Analyses of fruit traits and gene expression suggested that not only the condensation of soluble solids due to the reduction in fruit weight, but also changes in sugar metabolism may contribute to the increased Brix induced by coral sand and low phosphate.