Hemidesmus indicus (L.) R. Br. ex Schult. (Indian Sarsaparilla of the family Apocynaceae) is a perennial climber used in traditional and modern medicinal systems since ages due to presence of a phytoconstituent MBAlD (2-hydroxy 4-methoxy benzaldehyde) in its roots. The morphological and light microscopic examination of the foliar appendages of the in vitro regenerated plants revealed the presence of abnormalities in micro-morpho-anatomy of leaves, caused major shortfall to the acclimatization of in vitro raised plants and their survival success in the field. Therefore, the present study aimed to identify the effects of seismic stress treatment on the morphology, micro-morpho-anatomy and photosynthetic pigments development in tissue culture raised plants of H. indicus. The cultures were agitated at 80 rpm for 6.0 min using an incubator shaker for 4 wk twice a day. Significant phenotypic improvements with enhanced quality of shoots, roots and leaf number (14.0 ± 0.29), leaf area (3.2 ± 0.20 cm length and 1.0 ± 0.15 cm width), and growth ratio (4.8 ± 0.33 g fresh weight) were observed. The in vitro induced foliar micro-morpho-anatomical anomalies such as abnormal and non-functional stomata, underdeveloped cuticle, mesophyll tissues and vascular elements were mitigated by the seismic stress; and well organized tissues were developed. Seismic stress also enhanced the development of photosynthetic pigments in the leaves (8.20 μg g−1 FW) as compared with the control plantlets (6.89 μg g−1 FW). We postulate that the application of seismic stress alleviate in vitro induced morphological and anatomical anomalies at in vitro stage, and the developed plantlets exhibited improved survival rate during ex vitro and in vivo hardening processes.