Detailed structural models of di-cluster seven-iron ferredoxins constitute a valuable resource for folding and stability studies relating the metal cofactors’ role in protein stability. The here reported, hemihedric twinned crystal structure at 2.0Å resolution from Acidianus ambivalens ferredoxin, shows an integral 103 residues, physiologically relevant native form composed by a N-terminal extension comprising a His/Asp Zn 2+ site and the ferredoxin (βαβ) 2 core, which harbours intact clusters I and II, a [3Fe–4S] 1+/0 and a [4Fe–4S] 2+/1+ centres. This is in contrast with the previously available ferredoxin structure from Sulfolofus tokodai, which was obtained from an artificial oxidative conversion with two [3Fe–4S] 1+/0 centres and poor definition around cluster II.