Mangrove ecosystems store large amounts of soil organic carbon (SOC). However, degradation processes associated with invasive species can alter vegetation structure, hydrological conditions, and carbon cycling, with uncertain consequences for SOC storage and greenhouse gas emissions. This study evaluated changes in SOC stocks to 0–50 cm depth, soil CO₂, CH₄, and N₂O fluxes, and early restoration responses four years after ecological restoration in the Térraba–Sierpe National Wetland, Costa Rica. Comparisons were conducted among a conserved mangrove, a degraded mangrove dominated by Acrostichum aureum, and three restored sites subjected to hydrological rehabilitation with contrasting reforestation intensities. The degraded site showed significantly higher SOC contents (171 ± 31 Mg C ha⁻¹; p < 0.0001) compared to the conserved site (103 ± 26 Mg C ha⁻¹). CO₂ fluxes did not differ significantly between March and October. CH₄ and N₂O fluxes remained below the detection limits in most measurements. Redundancy analysis identified a significant association between vegetation composition and the measured environmental variables (p = 0.005). Higher CO₂ emissions were associated with the dominance of A. aureum. Plant density was positively related to SOC content (R² = 0.78). MR1 site, where hydrological rehabilitation was combined with high-density reforestation, had significantly higher SOC content than the degraded site (242 ± 24.3 Mg C ha⁻¹; p < 0.001). Soil CO₂ emissions at MR1 were also significantly lower than at the degraded site (p = 0.001). This study provides a pioneering field assessment of mangrove restoration through the control of A. aureum invasion. The results suggest that restoration design may influence soil carbon storage during the early stages of recovery.