In this study, we explored the capacity of different tomato rootstocks to improve the nutritional value of tomatoes grown in a greenhouse during the winter–spring period under low temperature and light conditions. The results showed that relative to nongrafted plants, some grafted rootstocks either did not affect or had detrimental effects on the nutritional parameters measured. In addition, the amount of serotonin was significantly lower in tomatoes from all grafted rootstocks than in tomatoes from the nongrafted plants. Nevertheless, relative to the nongrafted plants, some grafted treatments increased total macroelements (by 1.16 times), total microelements (by 1.43 times), protein content (by 17%), free total and essential amino acids (by respectively 23% and 19%), total phenolic compounds (by 11%), vitamin C (by 13.8%), lycopene (by 48%), and also total hydrocinnamic acids (by 67%) and flavonoids (by 279%). As the grafted treatments did not increase the tomato yield, we hypothesize that these compounds accumulated in the tomatoes due to the lack of increased biomass, which prevented a dilution effect on the compounds of interest in the fruits.