The micropropagation of critically endangered plant Crinum malabaricum Lekhak and Yadav (Malabar river lily) resulted in the development of in vitro-induced structural and physiological aberrations in the plantlets, which hampered the successful acclimatization and field establishment. Therefore, this study aimed to identify the effects of seismic stress on the morphoanatomical developments in tissue culture raised plantlets of C. malabaricum. The cultures were incubated for 4 weeks at 100 revolutions per min (rpm) for 8 min and twice per day. The mild mechanical agitation in the incubator shaker induced rapid changes in the morphology of stomata, epidermal cells, cuticular wax deposition, mesophyll cells, vascular elements, and development of air cavities in the leaves. It also improved the number of shoots (63.0 ± 0.16), leaf area (12.5 ± 0.24 cm length and 2.2 ± 0.18 cm width), number of roots (12.0 ± 0.20), and fresh weight (3.5 ± 0.29 gm) of plantlets per culture vessel. These parameters were reasonably elevated as compared to the non-stressed plantlets. The seismic stress also enhanced photosynthetic pigments ratio (7.36 ± 0.24 μg g −1 FW) and morpho-anatomical developments in the in vitro plantlets, and ultimately induced tolerance to withstand the stressful conditions of ex vitro and in vivo conditions. The study could help in improvement of the survival success of tissue culture raised plantlets via in vitro acclimatization. Thus, it could serve as a conservation strategy for this critically endangered and medicinally important plant species.