Background: Microbial ecosystems play a central role in regulating Earth’s biogeochemical cycles by mediating the transformation of carbon, nitrogen, sulfur, and phosphorus. Ongoing climate change—characterized by rising temperatures, altered precipitation patterns, ocean acidification, and permafrost thaw—is increasingly disrupting microbial community structure and metabolic functioning. These alterations have significant implications for greenhouse gas emissions and global climate feedback mechanisms. Objectives: This study aims to synthesize current scientific evidence on climate-driven changes in microbial ecosystems and to evaluate their impacts on global biogeochemical cycles, with emphasis on carbon and nitrogen dynamics across terrestrial and marine environments. Methods: A narrative review approach was employed, integrating peer-reviewed literature from major scientific databases. Studies involving field observations, experimental warming, molecular microbial analyses, and Earth system modeling were critically evaluated. Comparative assessment across ecosystems was conducted to identify consistent microbial responses and feedback patterns. Results: Climate warming significantly enhances microbial respiration and organic matter decomposition, leading to increased carbon dioxide emissions from soils. Hydrological variability alters nitrogen cycling pathways, promoting denitrification and nitrous oxide release. In marine systems, ocean warming and acidification reduce primary productivity and weaken biological carbon sequestration. Permafrost thaw mobilizes large carbon reservoirs, stimulating microbial methane production. Collectively, these responses intensify positive climate feedbacks and modify global elemental cycling. Conclusion: Microbial ecosystems are highly sensitive to climate change and actively regulate biogeochemical feedbacks that influence future climate trajectories. Incorporating microbial processes into Earth system models is essential for improving climate predictions. Long-term monitoring and integrated molecular–biogeochemical approaches are required to better understand microbial adaptation and to inform effective mitigation and ecosystem management strategies.