Background and aims <p>Pre-sprouted sugarcane seedlings are increasingly used to ensure uniform crop establishment; however, their performance is highly constrained by water deficit under climate change scenarios. This research evaluated whether a consortium of <i>Bacillus licheniformis</i> (FMCH001) and <i>Bacillus subtilis</i> (FMCH002) could mitigate drought stress by improving root development, soil microbial activity, and plant nutritional and physiological responses under different water regimes.</p> Methods <p>The experiment was conducted in a randomized block design using a 4 × 2 factorial scheme, with four water regimes (20, 40, 60, and 80% of field capacity) and two inoculation treatments (with and without bacteria), with four replicates.</p> Results <p><i>Bacillus</i> inoculation alleviated the adverse effects of water deficit, particularly under severe water restriction (20, 40, and 60% of field capacity), by increasing root length, surface area, volume, and diameter. Inoculated treatments showed higher arylsulfatase, β-glucosidase, acid phosphatase, and urease activities, indicating enhanced soil microbial functioning. These responses were associated with increased leaf concentrations of N, P, K, Ca, Fe, and Zn. Furthermore, inoculated plants exhibited improved photosynthetic performance, including higher PSII efficiency, electron transport rate, net CO₂ assimilation, water use efficiency, and carboxylation efficiency, contributing to better establishment and development throughout the sugarcane growth cycle.</p> Conclusion <p>Inoculation with <i>Bacillus subtilis</i> and <i>Bacillus licheniformis</i> mitigated the effects of water deficit in pre-sprouted sugarcane seedlings by promoting root development, enhancing soil microbial activity, and increasing nutrient acquisition, thereby improving plant mineral nutrition and photosynthetic performance.</p> Graphical Abstract <p></p>