A dated sediment core from an eutrophic mangrove area presented non-significant differences in carbon accumulation rates before (55.7 ± 10.2 g m− 2 yr− 1) and after three decades of deforestation (59.7 ± 7.2 g m− 2 yr− 1). Although eutrophication effects appear to compensate the loss of mangrove organic matter input, the results in this work show a threefold lower carbon accumulation than the global averages estimated for mangrove sediments. The effects of increasing eutrophication and enhanced sediment dry bulk density observed after deforestation (~ 30% higher) did not result in higher carbon stocks. Moreover, the lower TOC:OP (< 400) and C:N (~ 20) molar ratios, as well as increased nutrient accumulation, reflect the dominance of phytoplankton-derived organic matter after deforestation, resulting in less-efficient sedimentary carbon sinks. These results indicate that the organic material deposited from eutrophication may not compensate mangrove deforestation losses on carbon accumulation in mangrove ecosystems.