The study examines microbial communities and bioactive compounds in wild and cultivated populations of two medicinal plants, Tinospora cordifolia and Gynura procumbens, using metagenomic and metabolomic techniques. Bacterial communities in T. cordifolia and G. procumbens varied significantly between leaf and root. Leaves exhibited greater population-dependent variability, while root metabolomes remained more stable across populations. Multiple metabolites showed correlation patterns with specific bacterial phyla, suggesting functional relationships between plant chemistry and microbiota.