Rheum emodi Wall. ex Meisn is an important medicinal herb used in treating type II diabetes mellitus, arthritis, inflammation, and fever. Roots and rhizomes of this plant possess anthraquinones showing anticancer, antiviral, anti-inflammatory, anti-ulcerogenic, immunosuppressive, and pro-apoptotic activities. In the present study, in vitro propagation and adventitious root establishment were achieved for the detection and quantification of important secondary metabolites. In micropropagation experiments, high rate of callus induction was obtained from mid rib (100%) as well as leaf explants (97.67 ± 1.20%). The highest percent shoot induction was observed from leaf explants (76.25 ± 2.39%) as compared to callus (66.67 ± 2.20%). Regenerated shoots showed 70% rooting response with healthy long roots (5.73 ± 0.15 cm). Adventitious root culture response from nodal and leaf explants was better in liquid medium (93.33 ± 1.67% and 73.13 ± 2.87%) compared to semi-solid medium (85.0 ± 2.89% and 76.67 ± 3.33%). The highest DPPH (2–2 diphenyl, 1-picrylhydrazyl) free radical scavenging activity (92.73 ± 0.07%) and total antioxidant activity (6.24 ± 0.07 µg ascorbic acid equivalent (AAE) mg−1) was recorded in in vitro roots. Maximum phenol content (14.70 ± 0.29 µg gallic acid equivalent (GAE) mg−1) was present in adventitious root culture whereas flavonoid content (82.37 ± 0.12 µg quercetin equivalent (QE) mg−1) in in vitro shoots. The identification and quantification of secondary metabolites in in vitro shoots, invitro roots, and adventitious root cultures were evaluated via high-performance liquid chromatography-mass spectroscopy (HPLC–MS) analysis which revealed the presence of three anthraquinones, emodin, physcion, and chrysophanol, in adventitious root cultures. HPLC–UV detector analysis showed the highest emodin concentration (2.24%) in in vitro shoots. The present study gives a highly reproducible micropropagation protocol for R. emodi as well as provides an alternative source of anticancer compound, emodin, from in vitro shoots and root cultures.