Merdeka understands the impact of mining on the environment. Therefore Merdeka protects, conserves, monitors, and promotes the sustainable management of biodiversity around the mining operation area by involving independent parties. Monitoring of biodiversity includes terrestrial flora and fauna, freshwater aquatic biota, and marine aquatic biota.

Monitoring of biodiversity around the Tujuh Bukit mine in 2020 noted that the condition of fauna, flora, and freshwater, and marine biota was in a stable condition. The existence of 16 species of birds and 6 species of mammals are protected, indicating the quality of the forest in the Tujuh Bukit mine is in good condition and maintained. Monitoring the diversity of fauna and flora at the Wetar Island mine in 2020 also recorded good results.