The mangroves of Sulawesi have been subject to widespread deforestation and degradation, which has intensified since the 1980s. Despite efforts by government and community initiatives to restore these intertidal forests, comprehensive, long-term assessments of restoration outcomes are lacking. This study aims to enhance understanding of mangrove responses to significant environmental and human disturbances over the long-term, informing future restoration and management in North Sulawesi. Sedimentary records from two study areas were analyzed using palynology, microcharcoal, diatoms, and exploratory cryptotephra, and chronologically controlled via 14C and 210Pb dating as indicators of mangrove forest dynamics and resilience. This study presents an ∼8,000-year-old sediment record from a mangrove lagoon on Mantehage Island, Bunaken National Park, and two Late Holocene high-resolution sediment records, from two estuarine mangrove stands in Likupang. One site in Likupang was restored around 2003 CE following aquaculture pond establishment in the 1980s CE, while the other has no recent history of deforestation. Fossil pollen data shows mangroves dominated Mantehage lagoon for most of the last 8,000 years and Likupang since at least 1105 CE. Both areas experienced at least 18 disturbance events (volcanism, fire, storms, possible tsunamis, and human impacts), with mangroves showing varying resilience and full recovery of pollen abundance ranging from 14 to 903 years. Likupang’s mangrove is still recovering 16 years after restoration but shows compositional similarity to its pre-deforestation state. Mantehage’s mangrove is still recovering from a 14th-century seismic event which further reduced the ecosystem resilience to future natural and anthropogenic disturbances. Our findings indicate that both communities are on a trajectory towards the pre-disturbance state, based on pollen data, but may require management interventions to enhance resilience against future threats. This research provides a rare example of applying paleoecological methods to support restoration through long-term monitoring and offers a template for application in global mangrove conservation efforts.