Climate change-induced ocean warming is expected to greatly affect carbon dynamics and sequestration in vegetated shallow waters, especially in the upper subtidal where water temperatures may fluctuate considerably and can reach high levels at low tides. This might alter the greenhouse gas balance and significantly reduce the carbon sink potential of tropical seagrass meadows. In order to assess such consequences, we simulated temperature stress during low tide exposures by subjecting seagrass plants (Thalassia hemprichii) and associated sediments to elevated midday temperature spikes (31, 35, 37, 40 and 45ºC) for seven consecutive days in an outdoor mesocosm setup. During the experiment, methane release from the sediment surface was estimated using gas chromatography. Sulfide concentration in the sediment pore water was determined spectrophotometrically, and the plant’s photosynthetic capacity as Electron Transport Rate (ETR) and maximum quantum yield (Fv/Fm) was assessed using pulse-amplitude modulated (PAM) fluorometry. The highest temperature treatments (40 and 45ºC) had a clear positive effect on methane emission and the level of sulfide in the sediment and, at the same time, clear negative effects on the photosynthetic performance of seagrass plants. The effects observed by temperature stress were immediate (within hours) and seen in all response variables, including ETR, Fv/Fm, methane emission and sulfide levels. In addition, both the methane emission and the size of the sulfide pool were already negatively correlated to changes in the photosynthetic rate (ETR) during the first day, and with time, the correlations became stronger. These findings show that increased temperature will reduce primary productivity and increase methane and sulfide levels. Future increases in the frequency and severity of extreme temperature events could hence reduce the climate mitigation capacity of tropical seagrass meadows by reducing CO₂ sequestration, increase damage from sulfide toxicity, and induce the release of larger amounts of methane.