Sophora tonkinensis Gagnep., an important medicinal plant in karst rocky desertification areas, faces major growth and production challenges due to drought stress in its harsh habitat. Plant growth-promoting bacteria (PGPB) offer a promising strategy to enhance plant drought tolerance. This study investigated the efficacy of combined inoculation with an endophytic bacterial strain B29 and traditional bio-inoculant Azospirillum brasilense in alleviating drought stress in S. tonkinensis and explored the underlying mechanisms, with a focus on isoflavonoid biosynthesis. PGPB consortia significantly alleviated drought-induced oxidative damage throughout the stress period, reducing malondialdehyde content by 29.4 % and enhancing the activities of superoxide dismutase (108.8 %), peroxidase (38.7 %), ascorbate peroxidase (62.3 %), and polyphenol oxidase (9.73-fold). Concurrent increases in total phenolics (similar to 17.3 %) and flavonoids (similar to 27.6 %) were also observed. Metabolomic profiling revealed a significant promotion of isoflavonoid accumulation under drought stress, with eleven isoflavonoid metabolites (e.g., genistein, maackiain, mirificin) markedly upregulated (2.04- to 5.41-fold). Integrative transcriptomic and metabolomic analysis confirmed flavonoid/isoflavonoid biosynthesis as a critical mechanism for PGPB consortia-induced drought tolerance. Key structural genes for isoflavonoid synthesis (CHS, CHR, IFS, HID, HI4'OMT, I2'H, IFR, IF7MAT), along with five MYB transcription factors, acted as key regulators of this pathway. This study provides novel mechanistic insights into the role of specialised metabolism in PGPB-induced plant drought tolerance and suggests potential strategies for improving the cultivation of this valuable medicinal plant in water-limited environments.