Climate change has imposed a significant struggle for survival most of the Earth’s species, highlighting the urgent need for a healthy and secure environment. Recent scientific investigations have primarily concentrated on the development and use of microorganisms as powerful biotechnological tools to address the escalating pollution that poses a severe threat to life. But this microorganisims long-term effects on biodiversity and ecosystems remain a subject of inquiry. In this comprehensive review, we aim to thoroughly evaluate the effects of microorganisms on the general ecosystem and critically assess the use of existing biotechnological tools developed to combat climate-related challenges. By shedding light on the potential implications, this review strives to contribute to a deeper understanding of the intricate interplay between microorganisms, ecosystems, and climate change mitigation.