In this article, we challenge the notion that global warming stimulates organic matter mineralization and increases greenhouse gas emissions in lakes via direct temperature effects. We show that the interactive effects of warming and transparency loss due to eutrophication or browning overrides atmospheric warming alone. Thermal shielding enables 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 effects are strongest in shallow lakes where an additional burial of 4.5 Tg C yr⁻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 anoxia, 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.