Global methane emissions from natural wetlands and carbon release from permafrost thaw have a positive feedback on climate, yet are not represented in most state-of-the-art climate models. Furthermore, a fraction of the thawed permafrost carbon is released as methane, enhancing the combined feedback strength. We present simulations with an inverted intermediate complexity climate model, which follows prescribed global warming pathways to stabilization at 1.5 or 2.0 °C above pre-industrial levels by the year 2100, and which incorporates a state-of-the-art global land surface model with updated descriptions of wetland and permafrost carbon release. We demonstrate that the climate feedbacks from those two processes are substantial. Specifically, permissible anthropogenic fossil fuel CO2 emission budgets are reduced by 9–15% (25–38 GtC) for stabilization at 1.5 °C, and 6–10% (33–52 GtC) for 2.0 °C stabilization. In our simulations these feedback processes respond more quickly at temperatures below 1.5 °C, and the differences between the 1.5 and 2 °C targets are disproportionately small. This key finding holds for transient emission pathways to 2100 and does not account for longer-term implications of these feedback processes. We conclude that natural feedback processes from wetlands and permafrost must be considered in assessments of transient emission pathways to limit global warming. Climate feedbacks associated with wetland methane emissions and permafrost-thaw carbon release substantially reduce available carbon budgets to achieve temperature targets, suggest simulations with a climate–land-surface model system.