Sandalwood oil has been found in numerous therapeutic applications in traditional medicines such as Chinese traditional medicine and Ayurveda. However, there are no comparative accounts available in the literature that focused on in vitro and in vivo tree sample derived extracts. Combined dichloromethane and methanol extracts were obtained from in vitro samples, i.e., callus, somatic embryo, seedlings and in vivo from leaves of non-oil yielding young and oil-yielding matured trees. Phytochemical evaluation of the extracts reveals that the tree is rich in terpenoids, saponin, phenolics and tannins. The antibacterial properties of the five extracts were compared with sandalwood oil by screening against nine Gram negative and five Gram positive bacterial strains by disc diffusion, agar spot and TLC-bioautography methods. MIC for sandalwood oil was determined to be in the range of 0.078- 5 μg ml−1 for most test microorganisms screened. Bioautography results indicated the presence of potential antimicrobial constituents in somatic embryo extracts and sandalwood oil. Among the extracts screened, the somatic embryo extracts showed the strongest antibacterial activity comparable only to sandalwood oil and matured tree leaves extract. The findings presented here also suggest that apart from sandalwood oil, other parts of this tree across developmental stages are also enriched with antibacterial principles.