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Peatland restoration is widely used as a climate mitigation strategy, yet the immediate transition from a carbon source to a sink is rarely linear. While rewetting is intended to mitigate carbon loss, the precise biophysical mechanisms that govern carbon exchange during the early recovery phase remain poorly understood. This study employs an integrated multi-scale approach by combining eddy covariance, chamber-based fluxes, and Sentinel-2 remote sensing to track CO₂ dynamics through three distinct stages of restoration at a degraded peatland in Ireland. Our results show that restoration initially intensified CO₂ losses. During the active restoration phase, mean net ecosystem exchange (NEE) peaked at 0.62 µmol m⁻² s⁻¹ due to mechanical disturbance and peat oxidation. Following restoration, emissions declined and stabilized relative to the restoration phase at 0.56 µmol m⁻² s⁻¹, coinciding with a significant shift in energy partitioning. We observed a move from sensible heat dominance toward latent heat exchange, with the Bowen ratio dropping by 0.3, indicating a shift toward wetter surface conditions and evaporative cooling. Spatial analysis further highlights that while bunded areas remain emission hotspots, recolonized vegetation in the northern sections has already reached near-neutral CO₂ exchange. The negative correlation between NEE and NDVI (r = −0.48) indicates that biological recovery, rather than hydrological repair alone, plays a key role in carbon stabilization. These findings suggest that the system achieved "early functional stabilization" within just three years. This research provides a useful benchmark for peatland management, demonstrating that the transition to a carbon sink is a staggered process where microclimatic recovery precedes full biological sequestration.