Maximizing carbon sequestration in mangroves is part of the global effort to combat the climate crisis. However, methane (CH4) emissions can partially offset carbon sequestration in mangroves. Previous estimates have suggested that CH4 emissions offset organic carbon burial by 20% in mangroves with substantial freshwater inputs and/or in highly impacted mangroves. Here we resolve the magnitude and drivers of the mangrove CH4 offset using multiple isotopic tracers across a latitudinal gradient. CH4 emission offsets were smaller in high-salinity (~7%) than in freshwater-influenced (~27%) mangroves. Carbon sequestration was disproportionally high compared with CH4 emissions in understudied tropical areas. Low CH4 emissions were explained by minor freshwater inputs minimizing CH4 production in saline, high-sulfate conditions and intense CH4 oxidation in porewaters and surface waters. CH4 oxidation in mangrove surface waters reduced potential aquatic CH4 emissions by 10–33%. Overall, carbon sequestration through mangrove preservation and restoration is less affected by CH4 emissions than previously thought.