Mangroves are critical in the ecological, economic and social development of coastal rural and urban communities. However, they are under threat by climate change and anthropogenic activities. The Sunda Banda Seascape (SBS), Indonesia, is among the world’s richest regions of mangrove biomass and biodiversity. To inform current and future management strategies, it is critical to provide estimates of how mangroves will respond to climate change in this region. Therefore, this paper utilized spatial analysis with model-based climatic indicators (temperature and precipitation) and mangrove distribution maps to estimate a benchmark for the mangrove biomass of the SBS in six scenarios, namely the Last Inter-glacial Period, the current scenario (1950–2000) and all four projected Representative Concentration Pathways in 2070 due to climate change. Despite mangroves gaining more biomass with climate change (the increase in CO2 concentration), this paper highlighted the great proportion of below-ground biomass in mangrove forests. It also showed that the changes in spatial distribution of mangrove biomass became more variable in the context of climate change. As mangroves have been proposed as an essential component of climate change strategies, this study can serve as a baseline for future studies and resource management strategies.