Globally, mangroves sequester a large amount of carbon into the sediments, although spatial heterogeneity exists owing to a wide variety of local, regional, and global controls. Rapid environmental and climate change, including increasing sea-level rise, global warming, reduced upstream discharge and anthropogenic activities, are predicted to increase salinity in the mangroves, especially in the Bangladesh Sundarbans, thereby disrupting this blue carbon reservoir. Nevertheless, it remains unclear how salinity affects the belowground soil carbon despite the recognised effect on above ground productivity. To address this gap, research was undertaken in the Bangladesh Sundarbans to compare total soil organic carbon (SOC) across three salinity zones and to explore any potential predictive relationships with other physical, chemical properties and vegetation characteristics. Total SOC was significantly higher in the oligohaline zone (74.8 ± 14.9 Mg ha−1), followed by the mesohaline (59.3 ± 15.8 Mg ha−1), and polyhaline zone (48.3 ± 10.3 Mg ha−1) (ANOVA, F2, 500 = 118.9, p < 0.001). At all sites, the topmost 10 cm of soil contained higher SOC density than the bottom depths (ANOVA, F3, 500 = 30.1, p < 0.001). On average, Bruguiera sp. stand holds the maximum SOC measured, followed by two pioneer species Sonneratia apetala and Avicennia sp. Multiple regression results indicated that soil salinity, organic C:N and tree diameter were the best predictor for the variability of the SOC in the Sundarbans (R2 = 0.62). Despite lower carbon in the soil, the study highlights that the conservation priorities and low deforestation rate have led to less CO2 emissions than most sediment carbon-rich mangroves in the world. The study also emphasised the importance of spatial conservation planning to safeguard the soil carbon-rich zones in the Bangladesh Sundarbans from anthropogenic tourism and development activities to support climate change adaptation and mitigation strategies.