Abstract The present work is a continuation of our studies with iron pentacarbonyl, a model organometallic precursor for Focused Ion Beam-Induced Deposition (FIBID). Interactions of He2+(16 keV), Ne+(6 keV), Ne4+(40 keV), Ar2+(12 keV) and Ar8+(64 keV) projectile ions with [Fe(CO)5]n clusters are studied using TOF mass spectrometry. The clusters represent an intermediate between the gas phase and the bulk environment and can be used as a proxy for the processes in complex environments such as e.g. the nanostructure deposition. The addition of environment in the present study results in the observation of fragments with high kinetic energies ejected from clusters, an overall reduction of the fragmentation, and observation of a range of fragments associated with C-O bond dissociation, not observed for isolated molecules. On the other hand, the high efficiency of the Ne+ projectile in fragmenting the Fe(CO)5 isolated molecule is also observed in clusters.