In this article, we challenge the notion that global warming stimulates organic matter min-eralization and increases greenhouse gas emissions in lakes via direct temperature effects. We show that the interactive effects of warming and transparency loss due to eutrophica-tion or browning override effects of atmospheric warming alone. Thermal shielding ena-bles a longer and more stable stratification that results in bottom-water cooling, prolonged anoxia and enhanced carbon preservation in a large proportion of global lakes. These ef-fects are strongest in shallow lakes where an additional burial of 4.5 Tg C y-1 increases current global estimates by 9%. Despite more burial, the net global warming potential of lakes will increase via enhanced methane production, related to prolonged periods of an-oxia, rather than warming. Our understanding of how whole-lake carbon cycling responds to climate change needs revision, as the synergistic influence of warming and transparency loss has much broader ecosystem level functional consequences.