The Congo Basin, spanning over 3.7 million km2 across Central Africa, plays a critical role in regulating global climate, sustaining biodiversity, and supporting regional livelihoods. We explore the ecological functions of the Congo Basin ecosystems, emphasizing their role in the carbon cycle. We synthesize current knowledge on biogeochemical processes, carbon stocks, species interactions, and biodiversity patterns, while highlighting key data gaps and research needs. The region’s forests, soils, wetlands, and aquatic systems together form one of the world’s most significant carbon sinks, with unique characteristics, including high megafaunal density, extensive peatlands, and relatively low deforestation rates, shaping its contributions to carbon sequestration and climate regulation. We detail carbon cycle dynamics across lowland, montane, flooded, and savanna ecosystems and underscore the vast belowground carbon storage in the Cuvette Centrale peatlands. Patterns of alpha and beta tree species diversity affect ecosystem function and resilience, with plant functional traits playing a key role in nutrient cycling and productivity. Species such as forest elephants influence forest structure and carbon storage through seed dispersal and disturbance. Moreover, strong land-atmosphere feedbacks mean that evapotranspiration from the Congo Basin’s tropical forests plays a key role in shaping regional rainfall patterns. Land use and climate change pose growing threats to these functions, potentially triggering regime shifts and biodiversity loss. Ultimately, the Congo Basin remains underrepresented in ecological research and monitoring despite its global importance. Enhanced field-based and remote sensing efforts are urgently needed to inform integrated conservation and climate change mitigation strategies that account for both carbon dynamics and biodiversity.