The reactions of [Fe₃(CO)₁₂] or [Ru₃(CO) ₁₂] with RNC (R=Ph, C₆H₄OMe-p or CH₂SO₂C₆H₄Me-p) have been investigated using electrospray mass spectrometry. Species arising from substitution of up to six ligands were detected for [Fe₃(CO)₁₂], but the higher-substituted compounds were too unstable to be isolated. The crystal structure of [Fe₃(CO)₁₀(CNPh)₂] was determined at 150 and 298 K to show that both isonitrile ligands were trans to each other on the same Fe atom. For [Ru₃(CO)₁₂] substitution of up to three COs was found, together with the formation of higher-nuclearity clusters. [Ru₄(CO)₁₁(CNPh)₃] was structurally characterised and has a spiked-triangular Ru₄ core with two of the CNPh ligands coordinated in an unusual μ₃-η² mode. The substitution reactions of [M₃(CO)₁₂] by RNC have been investigated by electrospray mass spectrometry showing up to six COs can be replaced. [Fe₃(CO)₁₀(CNPh)₂] has both PhNC axially on the same Fe atom, and [Ru₄(CO)₁₁(μ₃-η²-CNPh)₂(CNPh)] has a spiked-triangular cluster core with two PhNC ligands in an unusual coordination mode.