Mangroves are under immense anthropogenic pressures globally which are further exacerbated by their accessibility to humans. To minimize human access hence pressures to the ecosystem, establishment of protected areas is often employed. However, the ecological effectiveness of protected areas, which influences their legal durability, is rarely assessed beyond curbing deforestation. Furthermore, little is known about whether protection could still provide a positive ecological impact if the sites are easily accessible, i.e., adjacent to urban areas, near roads, small in area and/or fragmented. To improve our understanding thereon, this study compares anthropogenic disturbance severity, forest structures and ecosystem carbon (C) stocks of protected and unprotected mangroves near Barranquilla, Colombia’s largest coastal city. The outcomes suggest that accessible, yet protected mangrove has a mean disturbance index of 5.3, lower than unprotected mangrove (mean 11). Protected mangrove also has higher mean (± SD) tree basal area (26.5 ± 15.6 m2 ha−1), mean densities of tree, sapling and seedling (899 ± 398, 5155 ± 7860, and 68,837 ± 73,899 individual ha−1, respectively) and biomass C stock (mean 89.5 ± 39 Mg ha−1) than those of accessible unprotected mangrove (mean basal area 19.3 ± 5 m2 ha−1; mean tree, sapling and seedling densities 823 ± 215, 749 ± 94, and 33,727 ± 44,882 individual ha−1, respectively; mean biomass C stock 60.2 ± 14.5 Mg ha−1). Results suggest that the current sediment C stocks, that is higher in unprotected than protected mangroves (396.8 ± 552.6 and 142.4 ± 205.7 Mg ha−1, respectively), are not primarily driven by conservation status, but by long-term processes that likely pre-date the protected status designation. Mangrove protection, however, could help maintain carbon stocks in soils and biomass and the potential for further soil carbon sequestration, and thus are pivotal in determining future trajectories of mangrove climate mitigation potential. This study shows that even imperfect protection offers ecological benefits to highly accessible ecosystems. Hence, focus should be placed on optimizing these benefits and minimizing their vulnerability to downgrading, downsizing and degazettement. •influence of protection on mangroves is assessed beyond curbing deforestation.•protection effectively limit anthropogenic disturbance on mangroves.•protection promotes mangrove biomass C and regeneration potential.•mangrove sediment C stocks is largely influenced by sediment properties.•mangrove protection is ecologically beneficial even for highly accessible systems.