Solanum lycopersicum is a vegetable with a high mineral, nutraceutical, and vitamin content. It is a basic ingredient in the human diet, and its use is diverse within the kitchen. Grafting and Ca, K, and Mg applications can be used to increase production and raise the mineral contents of tomato fruit. An experiment was established with tomato plants using the “CID F1” variety with the “FORTAMINO” rootstock, established in the NFT system, determining the influence on the agronomic yield and mineral composition of the fruit. Grafted and non-grafted plants were considered, with five concentrations (0-0-0, 9-0-0, 0-12-0, 0-0-9, and 9-12-9 mEq L−1) of Ca, K, and Mg, respectively. A highly significant difference was obtained in the grafted plants on high plants, number of leaves, number of fruits, polar diameters of fruits, equatorial diameters of fruits, and weight of fruits, with an increase in variables, FW 19% and NF 18%, and an improvement for the mineral composition in elements such as Ca 10%, P 1%, Mn 6%, Zn 7%, Cu 6%, Fe 64%, K 21%, and Mg 19%. The 9-12-9 meq formula improved Ca 6%, P 4%, Mn 12%, Zn 14%, Cu 8%, Fe 74%, and Mg 25%. The graft and the addition of calcium, potassium, and magnesium increased the mineral content in tomato fruits and improved the agronomic performance of the plants.