Opportunities to boost climate change mitigation and adaptation (CCMA) and sustainable conservation financing may lie in enhancing blue carbon sequestration, particularly in developing nations where coastal ecosystems are extensive and international carbon markets offer comparatively attractive payments for environmental stewardship. While blue carbon is receiving increased global attention, few credit-generating projects are operational, due to low credit-buyer incentives with uncertainty in creditable emissions reductions and high project costs. Little empirical guidance exists for practitioners to quantify return-on-investment (ROI) and viability of potential projects, particularly for rehabilitation where multiple implementation options exist with diverse associated costs. We map and model drivers of mangrove natural regeneration (NR) using remote sensing (high-resolution satellite imagery segmentation and time-series modeling), and subsequent carbon sequestration using field- and literature-derived data, across abandoned aquaculture ponds in the Philippines. Using project-specific cost data, we then assess ROI for a hypothetical rehabilitation-focused mangrove blue carbon project at a 9.68 ha abandoned pond over a 10-year timeframe, under varied rehabilitation scenarios [NR vs. assisted natural regeneration (ANR) with planting], potential emissions reduction accreditation methodologies, carbon prices and discount rates. NR was faster in lower-lying ponds with lower tidal exposure (greater pond dike retention). Forecasted carbon sequestration was 3.7- to 5.2-fold and areal “greenbelt” regeneration 2.5- to 3.4-fold greater in our case study under ANR than NR. Variability in modeled sequestration rates drove high uncertainty and credit deductions in NR strategies. ROI with biomass-only accreditation was low and negative under NR and ANR, respectively. ROI was greater under ANR with inclusion of biomass and autochthonous soil carbon; however, neither strategy was highly profitable at current voluntary market carbon prices. ANR was the only scenario that fulfilled coastal protection greenbelt potential, with full mangrove cover within 10 years. Our findings highlight the benefits of ANR and soils inclusion in rehabilitation-oriented blue carbon projects, to maximize carbon sequestration and greenbelt enhancement (thus enhance pricing with potential bundled credits), and minimize forecasting uncertainty and credit-buyers’ perceived risk. An ANR rehabilitation strategy in low-lying, sea-facing abandoned ponds with low biophysical intervention costs may represent large blue carbon CCMA opportunities in regions with high aquaculture abandonment.