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  Programmed electrochemical reconstruction converts FeNCN nanoclusters into Fe3 ensembles.
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  Operando XAFS reveals a stepwise FeNCN → Fe(OH)2 → FeO → Fe3 pathway.
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  Fe3 clusters achieve high Fe loading (∼12.2 wt%) with defined active sites.
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  Fe3@CNTs achieves 97.8% Faradaic efficiency for nitrate-to-ammonia conversion.

Electrochemical nitrate reduction to ammonia (NO3RR) enables sustainable NH3 production while valorizing nitrate-containing streams, yet creating high-loading, structurally defined active sites remains challenging. Here, we develop a programmed electrochemical reconstruction strategy that converts iron carbodiimide (FeNCN) nanoclusters on CNTs into Fe3 clusters (Fe3@CNTs) with a high Fe loading of ∼12.2 wt%. Operando X-ray absorption fine structure (XAFS) resolves a stepwise reconstruction pathway from FeNCN through Fe(OH)2 and FeO intermediates to Fe3 clusters, establishing a direct precursor–active site correlation. A size-defined catalyst series spanning single atoms, clusters, and nanoparticles enables a structure–activity relationship. Fe3@CNTs delivers a current density of 279.3 mA cm⁻2 and an NH₃ yield rate of 1.274 mmol h⁻1 cm⁻2 with 97.8% Faradaic efficiency. In situ spectroscopy and DFT calculations reveal that Fe3 clusters balance intermediate stabilization with moderated hydrogen supply, suppressing nitrite accumulation and hydrogen evolution. This study offers a mechanistic blueprint for reconstruction-guided catalyst design.