Tomato (Solanum Lycopersicum L.) is the most popular fruit crop worldwide. However, the deterioration of the flavor quality of commercial tomatoes is one of the main causes of consumer complaints. One of the most important factors influencing the synthesis of aromatic compounds in tomato is the growing medium, though studies on the effect of the growing substrate on its volatile profile are limited. Therefore, the main objective of this work was to improve the aromatic and flavor properties of tomato through the use of novel growing media obtained from the remains of Posidonia oceanica (PO), favoring the revalorization of residues. A greenhouse experiment was carried out in pots with tomato seedling cv. sweet cherry with three treatment groups—control (50% peat–50% perlite), PO (50% PO washed/sieved–50% perlite), and IP (50% PO unaltered–50% perlite)—for 9 weeks under controlled temperature conditions (18°C/27°C (night/day)), 60% relative humidity, and two daily irrigations of 100 mL with tap water. To evaluate the effectiveness of the treatments, fresh weight, total soluble solids, and the concentrations of organic and volatile compounds were measured by SPME-GC/MS. The average weights of the fruits obtained were 4.97, 5.77, and 4.65 g, and they had sugar contents of 8.7, 7.4, and 10.0 ºBx for the control, PO, and IP groups, respectively. This variation was due to the high salinity of the IP sample, which resulted from not washing away the salts from the Posidonia oceanica debris, favoring the production of sweeter, although smaller, tomatoes. Among the volatile compounds identified by SPME-GC/MS, it stands out that the tomatoes from the IP substrate, followed by PO and the control, presented the highest concentrations of octanal and hexyl acetate, conferring citrusy, fresh, and sweet aromas. Additionally, the tomatoes from PO also had a notable concentration of nonanal and alpha-terpineol, contributing to their herbal and fresh notes.