The commercial-scale production of Caralluma tuberculata faces significant challenges due to lower seed viability and sluggish rate of root growth in natural conditions. To overcome these obstacles, using phyto-mediated selenium nanomaterials as an in vitro rooting agent in plant in vitro cultures is a promising approach to facilitate rapid propagation and enhance the production of valuable therapeutic compounds. This study aimed to investigate the impact of phytosynthesized selenium nanoparticles (SeNPs) on the morphological growth attributes, physiological status, and secondary metabolite fabrication in in vitro propagated Caralluma tuberculata. The results demonstrated that a lower dose of SeNPs (100 μg/L) along with plant growth regulators (IBA 1 mg/L) had an affirmative effect on growth parameters and promoted earliest root initiation (4.6±0.98 days), highest rooting frequency (68.21±5.12%), number of roots (6.3±1.8), maximum fresh weight (710±6.01 mg) and dry weight (549.89±6.77 mg). However, higher levels of SeNPs (200 and 400 μg/L) in the growth media proved detrimental to growth and development. Further, stress caused by SeNPs at 100 μg/L along with PGRs (IBA 1 mg/L) produced a higher level of total chlorophyll contents (32.66± 4.36 μg/ml), while cultures exposed to 200 μg/L SeNPs alone exhibited the maximum amount of proline contents (10.5± 1.32 μg/ml). Interestingly, exposure to 400 μg/L SeNPs induced a stress response in the cultures, leading to increased levels of total phenolic content (3.4 ± 0.052), total flavonoid content (1.8 ± 0.034), and antioxidant activity 82 ± 4.8%). Furthermore, the combination of 100 μg/L SeNPs and plant growth regulators (1 mg/L IBA) led to accelerated enzymatic antioxidant activities, including superoxide dismutase (SOD = 4.4 ± 0.067 U/mg), peroxidase dismutase (POD = 3.3 ± 0.043 U/mg), catalase (CAT = 2.8 ± 0.048 U/mg), and ascorbate peroxidase (APx = 1.6 ± 0.082 U/mg). This is the first report that highlights the efficacy of SeNPs in culture media and presents a promising approach for the commercial propagation of C. tuberculata with a strong antioxidant defense system in vitro.