The effect of scopoletin-standardized Morinda elliptica leaf extract against osteoarthritis was investigated in ex vivo explant culture and preclinical rodent model. Thirty male rats were grouped (n = 6) into untreated osteoarthritis (OA), OA + Diclofenac (5 mg/kg), and OA + extract (200 and 400 mg/kg) and compared with healthy control. Monosodium iodoacetate were injected into the right intra-articular knee joints to induce OA. The rats were evaluated for OA severity via physical (micro-CT and histological observations), biochemical, ELISA, and mRNA expression analysis (for inflammation and cartilage degradation biomarkers), after 28 days of treatment. The extract suppressed glycosaminoglycan release from the cartilage explant in the presence of Interleukin-1β. The 200 mg/kg dose appeared better than 400 mg/kg dose, at reducing cartilage and subchondral bone erosions in OA-induced rats, by significantly down-regulating the collagenases and aggrecanase. The extract dose-dependently reduced serum inflammation biomarkers and increased bone formation biomarkers to near normal levels in the OA-induced rats. M. elliptica leaf scopoletin-standardised extract alleviated OA progression and articular cartilage structure, by ameliorating cartilage degradation, nitric oxide levels, inflammation, bone /cartilage homeostasis, collagenase/aggrecanase activities, chondrocytes survival, subchondral bone structure and integrity.