(1) Background: The effects of Zn and caffeine as promoters of fruit quality in the Solanum lycopersicum L. cultivar 'Panarea' were tested. (2) Methods: During the 56 days of the experiment, plants were treated weekly with 100 mL of 1 mM Zn (Zn), 1 mg L-1 caffeine trimethyl-13C (caffeine), and 1 mM Zn + 1 mg L-1 caffeine trimethyl-13C (Zn + caffeine) and compared to plants that were given tap water (control). (3) Results: Caffeine was taken up by the roots and translocated to the leaves, which positively influenced the number of fruits per plant. After 56 days of treatment, Zn induced a positive increase in tomato dry weight, reducing shoot length (-16.7%) compared to the other treatments. Zn + caffeine had a positive effect on the phenylpropanoid pathway of fruits, and 4-coumaric acid, caffeic acid, and t-ferulic acid were significantly increased, as well as the total antioxidant capacity of the tomatoes. In the flavonoid pathway, only apigenin and luteolin contents were reduced by treatments. The tomatoes showed similar concentrations of the mineral elements Cu, Mn, Fe, Na, Ca, Mg, and K. The Zn and caffeine target hazard quotients were <1, indicating that health risks via the consumption of these tomatoes did not occur. (4) Conclusions: Tomato plants could be irrigated with water containing lower values of Zn, caffeine, and a combination of the two. The treated fruits are rich in antioxidant compounds, such as coumaric acid, caffeic acid, and t-ferulic acid, which are beneficial for human health. No considerable health risks associated with human consumption have been detected.