Black gram [Vigna mungo (L.) Hepper] is a popular pulse crop in Asia that is severely affected by drought stress. It is known that the application of pink pigmented facultative methylotrophic bacteria (PPFM) enhances drought tolerance in agricultural crops. An experiment was conducted to explore the metabolomic profile associated with the foliar application of PPFM on drought stressed black gram plants. Spectrophotometric analysis revealed an increase in the osmolytes, fructan (6.50 mg/g) and proline (3.45 μM/g) in the leaf of PPFM treated plants under drought stress. Also, this treatment showed a high accumulation of antioxidants, carotenoids (45.63 μg/g) and tocopherol (9.67 μg/g) and significantly increased the grain yield. Gas chromatography-Mass Spectroscopy (GC-MS) analysis detected 34 metabolites in the PPFM treated leaves under drought stress of which the sugars, fructose, beta-D-allopyranose and beta-D-galactopyranose showed high accumulation. Nine metabolic pathways were found to be affected of which the glyoxylate and dicarboxylate metabolic pathway was most impacted. The results can facilitate further dissection of the mechanisms of drought tolerance contributed by PPFM.