Background and aims <p>Soybean is a globally important crop with socioeconomic importance worldwide. Magnesium (Mg) nutrition may activate plant defenses against drought but its role in soybean remains poorly understood. Our goal was to provide metabolic and molecular evidence through which Mg supplementation helps in healing drought damage and promotes growth recovery in a drought-sensitive soybean cultivar.</p> Methods <p>A field experiment was conducted to compare two water regimes based on the soil’s water retention capacity (well-irrigated and drought), two soybean cultivars (M8808 and TMG1180) and two Mg levels (recommended and supplementation). Growth, water status, oxidative stress, organic compounds, Mg content and metabolic profile were evaluated.</p> Results <p>Drought markedly reduced biomass accumulation and leaf succulence, particularly in M8808 cultivar, classified as drought sensitive, compared with the drought-tolerant TMG1180. However, Mg supplementation improved biomass and water status in sensitive M8808 cultivar, resulting in a higher drought tolerance index. In contrast, TMG1180 plants showed similar performance under both drought and well-irrigated conditions, suggesting inherent drought tolerance. The superior performance of Mg-supplemented M8808 plants was associated with increased proline accumulation, which likely alleviated oxidative damage in leaves, evidenced by decreased H₂O₂ and MDA levels, and acted as a compatible solute to limit water loss. The coordinated regulation of key metabolites, including asparagine, shikimic acid, citric acid, sorbitol, malic acid, and malonic acid, appears to underpin metabolic adjustments that counteract the drought-induced restrictions.</p> Conclusion <p>The findings provide insights into the metabolic mechanisms underlying the complex interaction between Mg supplementation and soybean responses to water deficit.</p>