Conservation and restoration of mangroves are necessary to meet global commitments for tackling the climate and biodiversity crises as well as reducing poverty. Management success is typically evaluated by estimating changes in vegetation cover, while changes in species composition and structural attributes across different habitats are often not considered. Here, we evaluated changes in mangrove composition, structural attributes, and drivers of change across Physically Stable Habitat (PSH), Diminished Tidal Inundation Habitat (DTIH), and Poor Drainage Habitat (PDH), for mangroves that have been protected for 22 years. We also analyzed the most likely ecological processes involved in the changes that have occurred. After 22 years, species remained the same in PSH and DTIH, but Rhizophora apiculata and Lumnitzera racemosa disappeared in PDH. Changes in relative proportions (number of trees of a species: total number of trees), and species abundance, varied between habitats. Additionally, changes in structural attributes also differed between habitat types over time suggesting they were driven by distinct ecological processes. Vegetation changes in PSH most likely occurred through a combination of ecologically important mangrove forest replacement and gap recovery processes, compared to only the gap recovery process in DTIH, and episodic changes due to stressful environmental conditions in PDH. Restoring hydrology, preventing sedimentation, planting proper seedlings of Avicennia marina should be conducted to save species and mangrove sustainability in PDH. It is highly recommended that managers follow a habitat-based approach to achieve effective management. •Assessing habitat changes reveals diverging mangrove trajectories missed by traditional methods.•By adopting a habitat-based approach, managers can make more efficient and targeted interventions.•A habitat-based approach is adaptable for diverse mangrove areas and therefore could aid conservation globally.