The aim of this research was to determine the impact of hydrogen peroxide spraying and ozone gas fumigation during the growing season of tomato plants grown under cover on the mechanical and chemical parameters of fruit harvested from these plants. Tomato plants were grown under cover in accordance with the principles of good agricultural practice in the soil and climatic conditions of southeastern Poland. During the growing season, tomato fruits were collected for testing in order to determine the impact of the applied variable factors on the modification of selected metabolic pathways of bioactive compounds. As part of the tests on the chemical properties of the fruits, the content of ascorbic acid, the total content of polyphenols, and the antioxidant potential were determined. Additionally, the influence of the tested variable factors on the mechanical properties of tomato fruits was determined. In the case of the total polyphenol content, the most beneficial effects were observed for fruits collected from plants treated with ozonation at a dose of 2 ppm for 3 min and spraying the plants with 1% hydrogen peroxide. The highest antioxidant potential was recorded for fruits of the variants ozonated with doses of 2 ppm for 1 min, 2 ppm for 1.5 min, and 2 ppm for 3 min compared to the remaining variants and controls. In turn, the vitamin C content increased significantly in the tested fruits after the ozonation of plants with a dose of 2 ppm for 1 min and ozonation with a dose of 2 ppm for 3 min combined with spraying plants with 3% hydrogen peroxide. In the case of the mechanical properties of tomato fruits, only the ozonation dose of 2 ppm for 3 min significantly improved them.