Estuarine sediments make an important contribution to the global carbon cycle, but we do not know how this will change under a future climate, which is expected to have lower pH oceans and frequent high‐temperature days. Six combinations of warming and partial pressures of CO2 (pCO2) were chosen to investigate the combined and individual effects of short‐term pressures on the diel metabolic response of shallow unvegetated sediments ex‐situ. Whereas warming significantly increased respiration, making sediments more heterotrophic, high‐pCO2 increased net primary productivity, resulting in less heterotrophic sediments. As a result, warming decreased the carbon burial potential of estuarine sediments and high‐pCO2 had the opposite effect. High‐pCO2 mitigates the negative effects of warming on benthic metabolism under the combined scenario, with carbon burial similar to that expected under high‐pCO2 conditions alone. Climate scenarios also changed the diurnal pCO2 variation, with ranges increasing by 33% with warming, and almost doubling under high‐pCO2 conditions. An additive response in pCO2 variability was observed under the combined scenario, increasing to 2.3× the current diel‐pCO2 range, highlighting the reduced buffering capacity of the water associated with a high CO2 climate. Future carbon burial and export under increased frequencies of unseasonably warm days projected for mid and end of century (30% and 50% of days‐per‐year, respectively) were estimated with and without ocean acidification. By 2100, warming alone could decrease annual estuarine sediment burial potential by 25%. However, ocean acidification could mitigate the negative effects of more frequent high‐temperature days and increase carbon burial potential over current conditions by ~18%.