Abstract Ocean warming and the loss of larger (often predatory) fauna are major threats to seabed (benthic) ecosystem functioning. Yet, we know little about the combined effects of warming and faunal species loss upon the marine carbon cycle. Using stable isotope pulse‐chase experiments, we tested how faunal species loss affects microbial carbon sequestration and retention in intertidal sediments, under both ambient and predicted future warming conditions (ambient +2°C), using the shore crab Carcinus maenas as a model predator. We traced the fixation and retention of a fixed dose of 13C‐labelled sodium bicarbonate within sediment organic matter and microbial biomass. Carcinus presence was associated with higher total organic carbon concentration within the mesocosm sediments. Temperature had no significant effect upon sediment total organic carbon concentrations. Temperature and Carcinus presence had no significant effect on polar lipid fatty acid (PLFA) concentrations within the sediment, which is a proxy for microbial biomass. Carcinus presence increased retention of 13C‐labelled carbon within the sediment organic matter pool under future warming conditions. Retention of the 13C‐label within the microbial PLFAs decreased significantly under future warming conditions. Changes in the relative abundance of PLFAs revealed increased contribution of microeukaryotes to the microbial community under ambient conditions, in the absence of Carcinus. PLFA profiles revealed significant changes in 13C‐label retention within the bacteria and microeukaryotes, driven by interactions between Carcinus presence and temperature. Given that temperature is a fundamental control on the metabolic activity of marine organisms (from bacteria to metazoans), we propose that interactions between faunal species loss and ocean warming will have a pronounced effect upon marine carbon budgets. A plain language summary is available for this article.