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 2.0 Å 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.