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<i>Nardostachys jatamansi</i> is a critically endangered medicinal plant and endemic to the Himalayas, having high commercial demand globally. The accumulation of various secondary metabolites in its shoots and roots with antioxidant potential are well-documented in traditional as well as modern medicine systems. In the present study, we first attempted to investigate the impact of citrate (−ve charge, 11.1 ± 1.9 nm) and CTAB (+ve charge, 19.5 ± 3.2 nm) coated gold nanoparticles (AuNPs) on the in vitro proliferation and antioxidant activities of <i>N. jatamansi</i>. Both the nanoparticles differentially affected the morphological and biochemical parameters, chlorophyll content, internal hormone concentration, and antioxidant activities in a concentration-dependent (10–100 µM) manner. Vigorous shooting was observed in half strength MS medium supplemented with IAA (1 mg/L) with 60 µM citrate-AuNPs (46.4 ± 3.7 mm) and 40 µM CTAB-AuNPs (42.2 ± 3.2 mm). Similarly, the maximum number of roots (5.00 ± 0.67 and 5.33 ± 0.58) and root length (29.9 ± 1.5 mm and 27.3 ± 4.8 mm) was reported in half-strength MS medium with IAA (1 mg/L) supplemented with 60 µM citrate-AuNPs and 40 µM CTAB-AuNPs, respectively. In addition, plants growing on MS medium supplemented with 60 µM citrate-AuNPs and 40 µM CTAB-AuNPs showed significantly enhanced photosynthetic pigments (chlorophyll a and b, carotenoids, and total chlorophyll), internal hormone concentration (GA3, IAA, and ABA), and antioxidant activities (total phenolics, flavonoids, DPPH, and SOD enzyme activity). Moreover, the transcript analysis of <i>ANR1</i>, <i>ARF18</i>, <i>PLY9</i>, <i>SAUR28</i>, <i>GID1A</i>, <i>GRF1</i>, <i>SOD</i>, and <i>CAT</i> further confirmed the role of 60 µM citrate-AuNPs and 40 µM CTAB-AuNPs in the improvement in the growth and antioxidant activities of <i>N. jatamansi.</i> Bearing in mind the urgent requirements of the effective conservation measures of this endangered species, the present findings suggest the elicitation of citrate-AuNPs and CTAB-AuNPs would significantly improve the potential applications of <i>N. jatamansi</i> in the medicinal plant-based industry.