Seagrass ecosystems are globally-significant ‘blue carbon’ sinks; however, there is concern that this capacity will decline if rising ocean temperatures accelerate microbial decomposition. Decomposition of plant litter is a key process in the global carbon cycle—it influences how much carbon is available for sequestration. Therefore, understanding the biogeochemistry underlying decomposition is essential to predicting the capacity of seagrass ecosystems to act as carbon sinks in the future. Here, we tracked the breakdown of standardised and natural litter of varying chemical recalcitrance (rooibos tea > seagrass leaves > green tea) combined with highly-sensitive microsensor technology to test (a) how elevated water temperatures affect short-term microbial turnover, and (b) provide novel information on how the decay dynamics of the tea litter compare to those of natural litter. We found that increased temperatures (+ 5–10 °C) boosted microbial activity for all substrates, exhibited as enhanced decay, oxygen consumption and sulphate reduction. Within the 1-month experiment, the green tea litter had a rapid Q10 response to the temperature increase, quickly exhausting the resources for microbes, while the response of the rooibos tea and seagrass litters became more apparent toward the end of the experiment. Our results suggest that the tea litters capture a range of decomposition traits and can be compared with natural litter using traditional exponential decay models. The enhanced temperature-driven organic matter turnover, even under anoxic conditions, highlights the vulnerability of fresh litter to microbial attack during the early stages of decay and the potential weakening of blue carbon accumulation rates under future climatic conditions.