<p>This research focused on improving the drought tolerance of <i>Dracocephalum moldavica</i>, a plant vulnerable to water stress, by exploring the combined effects of melatonin spray and mycorrhizal fungus <i>Glomus intraradices</i> inoculation. The experiment was designed as a factorial randomized study to evaluate the plant’s morphological, physiological, and phytochemical responses under different drought conditions (100%, 75%, and 50% field capacity). The findings revealed that the combination of melatonin and mycorrhizal inoculation significantly improved the morphological traits of Moldavian balm under drought conditions. Under severe drought (50% field capacity), chlorophyll a and b levels increased by 26.3% and 35.5%, respectively, when both treatments were applied. Stress indicators, including electrolyte leakage and malondialdehyde content, were substantially reduced with the simultaneous application of melatonin and mycorrhizal symbiosis, indicating decreased cellular damage. Moreover, the combined treatment resulted in the highest activities of the antioxidant enzymes catalase and peroxidase, suggesting that these treatments bolster the plant’s oxidative stress defense mechanisms. Additionally, drought stress alone led to an increase in secondary metabolites like phenolic and flavonoid compounds, which were further amplified by the treatments. The study also observed significant alterations in the essential oil composition of the plant. Drought stress increased the levels of α-pinene, 1,8-cineole, and borneol, and these increases were even more pronounced with the combined treatments. Conversely, the levels of geraniol and geranial decreased under drought stress and further with treatment. Overall, this research demonstrates that melatonin and <i>Glomus intraradices</i> inoculation can effectively enhance drought tolerance in <i>Dracocephalum moldavica</i> by improving its physiological characteristics and biochemical composition.</p>