The high growth-stimulating effect of plant extract has urged the plant biotechnologists to use natural supplements in the culture media instead of synthetic phytohormones. We advocated the effect of sprouted sorghum extract (SSE) on emergence, in vitro acclimatization, and genetic fidelity in coleoptile derived callus of indica rice variety ADT36. The use of SSE with Murashige Skoog medium efficiently acclimatized the root and shoot apical systems. A higher mat and seminal roots (3.4 g biomass) with an efficient shoot primordium elongation were observed with an increase in the concentration of SSE. Seeds treated with SSE medium showed higher germination and earlier coleoptile maturation about 48 h compared to untreated seeds, and there was a higher expression of eEF-1α with an increase in coleoptile length. B5 medium was effective on inducing embryogenic and nodular callus from 3-day-old coleoptile with 3.0 mg/L 2,4-dichlorophenoxyacetic acid and further proliferated effectively with 0.8 mg/L kinetin with a fresh weight of 180 mg. Highly significant regeneration was observed with combination of 2.5 mg/L 6-benzylamino purine and 3.0 mg/L α-naphthaleneacetic acid. The metabolic and genetic profiles of in vitro and directly cultivated plants were the same, examined through Fourier-transform infrared spectroscopy, random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and R-ISSR (combination of RAPD and ISSR) markers, respectively, and thus confirming the significant efficacy of the SSE incorporated medium. Disarmed T-DNA was transformed to coleoptile derived callus through Agrobacterium tumefaciens LBA4404 and confirmed by GUS assay. The T-DNA integration was confirmed by DNA blot analysis using DNA from transient GUS-expressed explants. Thus, SSE can be used as a natural and organic supplement for organogenesis and efficient acclimatizations of shoot and root apical meristems in regenerated plants.