Coelogyne mooreana Sander ex Rolfe, a valuable, rare, and endemic orchid species of the Vietnamese flora, is characterized by high ornamental qualities. This orchid is highly ornamental and often referred to as the “queen” of the genus Coelogyne due to its large, white, fragrant flowers adorned with black spots and a central yellow stripe. Therefore, this study aimed to develop a protocol for clonal micropropagation by modifying the nutrient medium with organic additives and plant growth regulators. Immature seeds collected from unopened fruits six months after artificial pollination were used as starting material. This work involved several stages: asymbiotic seed germination, protocorm development, seedling formation, and rooting. The highest seed germination rate (93%) was achieved on Gamborg (B5) nutrient medium supplemented with 0.5 mg/L 6-BAP. Maximum adventitious shoot formation was observed on Murashige and Skoog (½ MS) nutrient medium with organic additives but without plant growth regulators (5.64 and 4.56 shoots, respectively). Favorable results for protocorm development and seedling formation were obtained on ½ MS medium supplemented with 0.5 mg/L 6-BAP and coconut water (100 mL/L). At the rooting stage, the most effective medium was ½ MS supplemented with 0.5 mg/L IBA and 100 mL/L coconut water, which promoted the development of a strong root system, with a rooting percentage of 96.7%, 5.05 ± 0.36 roots per explant, a root length of 2.43 ± 0.05 cm, and a plant length of 5.95 ± 0.24 cm. Seedlings planted in a 1:1:1 ratio of bark, perlite, and peat exhibited high viability when adapted to ex vitro conditions. For the first time, a complete protocol for clonal micropropagation of C. mooreana encompassing all stages was developed. These results provide recommendations for the conservation and mass propagation of this rare and valuable orchid species.