The isomerization of iridium(III) complexes with metalated N-heterocyclic carbene (NHC) ligands was studied. The fac isomers of complexes with 1-phenyl-3-methylbenzimidazolin-2-ylidene or 1-phenyl-3-benzylbenzimidazolin-2-ylidene ligands are transformed cleanly into the mer isomers when solutions of the complexes are treated with first HNTf2 and then NEt3. The transformation can be accomplished within a few minutes and the side product (NEt3H)(NTf2) is easy to separate. Spectroscopic and structural analyses indicate that the isomerization proceeds by protonation of the carbene ligand at the metalated phenyl group, accompanied by a fac → mer rearrangement of the carbene donors. An iridium complex with a 1-phenyl-1,2,4-triazolo[4,3-f]phenanthridine-based carbene ligand could not be isomerized under similar conditions, most likely because of its reduced conformational flexibility.