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<i>Moringa oleifera</i> is a rich source of polyphenols whose contents and profile may vary according to environmental conditions, harvest season, and plant tissue. The present study aimed to characterize the profile of phenolic compounds in different tissues of <i>M. oleifera</i> grown under different temperatures (25, 30, and 35 °C), using HPLC/MS, as well as their constituent phytochemicals and in vitro antioxidant activities. The in vitro antioxidant activity of the extracts was evaluated using the 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2-azino-bis-3-ethylenebenzothiozoline-6-sulfonicacid (ABTS), and ferric-reducing antioxidant power (FRAP) methods. The polyphenolic compounds were mainly found in the leaves at 30 °C. UPLC/QTOF-MS allowed for the identification of 34 polyphenolic components in seedlings, primarily consisting of glucosides, phenols, flavonoids, and methoxy flavones. At 30 °C, the specific activities of antioxidative enzymes were the highest in leaves, followed by seedlings and then seeds. The leaf and seed extracts also exhibited a greater accumulation of proline, glycine betaine, and antioxidants, such as ascorbic acid, and carotenoids, as measured by the inhibition of ROS production. We found that changes in the expression levels of the validated candidate genes <i>Cu/Zn-SOD</i>, <i>APX</i>, <i>GPP</i>, and <i>TPS</i> lead to significant differences in the germination rate and biochemical changes. These findings demonstrate that <i>M. oleifera</i> plants have high concentrations of phytochemicals and antioxidants, making them an excellent choice for further research to determine their use as health-promoting dietary supplements.