Soil moisture is a challenging environmental factor adversely affecting the growth of plants under water stress conditions. To cope with water scarcity, plants compromise their growth and switch on their adaptive machineries; however, responses vary with species. How water stress affects Aquilaria malaccensis and how to mitigate water stress to keep the optimum growth of the plant is of high importance considering the socio-economic value of the species. Therefore, this study aimed to investigate the efficacy of environmentally friendly mitigation measures of water stress by applying biochar, Bacillus altitudinis (PGPR) and Trichoderma asperellum. The results showed that the seedling of Aquilaria exhibited comparable growth performances under water stress conditions with the application of biochar and the two microbes. Stress was alleviated by reducing the oxidative damage of Reactive Oxygen Species (67.63%) and Malondialdehyde (58.78%) and elevating the accumulation of proline (39.72%) in the single or combined treatments of biochar, PGPR and Trichoderma. Consequently, the photosynthesis pigment chlorophyll (43.89%) and stomatal conductivity (50.71%) increased in the treated plants grown under water stress. Applying biochar, PGPR and Trichoderma asperellum reduced H₂O₂ (67.63%) and MDA (58.78%) levels and helped to accumulate proline (39.72%), reducing oxidative damage. On the other hand, the photosynthesis pigment chlorophyll (43.89%) and stomatal conductivity (50.71%) helped increase gas exchange and the photosynthesis rate. This study highlights a promising result for enhancing Aquilaria malaccensis resilience to drought conditions for its sustainable production in arid and semi-arid areas.