Red Sea mangroves have a lower carbon burial rate than the global average, whereby small greenhouse gas fluxes may offset a large proportion of carbon burial. Monthly soil core sampling was conducted across 2 years at two sites within a central Eastern Red Sea mangrove stand to examine carbon dioxide (CO2) and methane (CH4) fluxes under dry and inundated conditions. Fluxes were highly variable, characterized by a prevalence of low emissions punctuated by bursts of high emissions. At the landward site, average±SE (median) flux from the soil-air interface was 3111±929 (811) µmol CO2 m− 2 d− 1 and 1.68±0.63 (0.26) µmol CH4 m− 2 d− 1 under light conditions, and 8657±2269 (1615) µmol CO2 m− 2 d− 1 and 0.84±0.79 (0.59) µmol CH4 m− 2 d− 1 under dark conditions. Average±SE (median) sea-air fluxes were–55±165 (-79) µmol CO2 m− 2 d− 1 and 0.12±0.23 (0.08) µmol CH4 m− 2 d− 1 under light conditions, and 27±48 (53) µmol CO2 m− 2 d− 1 and 0.16±0.13 (0.09) µmol CH4 m− 2 d− 1 in dark conditions. The seaward site recorded higher CH4 flux, averaging 18.7±8.18 (1.7) and 17.1±4.55 (7.7) µmol CH4 m− 2 d− 1 in light and dark conditions. Mean fluxes offset 94.5% of carbon burial, with a median of 4.9% skewed by extreme variability. However, reported CO2 removal by total alkalinity emission from carbonate dissolution greatly exceeded both processes and drives the role of these ecosystems as intense CO2 sinks.