The formation of bcc and fcc during the coalescence of free and supported Fe and Ni clusters has been studied by molecular dynamics simulation using an embedded atom method. Structural evolution of the clusters, coalesced under varying temperature, Ni content and substrate conditions, was explored by interatomic energy, snapshots, pair distribution functions and bond order parameters. The results show that the formation of bcc and fcc is strongly related to Ni content, substrate and coalescence temperature. Free clusters coalesced at 1200 K form bcc at lower Ni contents with fcc forming at higher Ni concentrations and no observable coexistence of bcc and fcc. Differences in coalescence at 1000 K result from the coexistence of bcc and fcc within the Ni range of 50-70%. Free clusters supported on disordered Ni substrates were shown to transform from spherical morphology to islands of supported clusters with preferred epitaxial orientation. The Ni content required to form bcc and fcc coexistence on supported clusters at 1000 K decreased to 30-50% Ni. Free clusters possessing bcc and fcc generally stacked along the bcc (110) and fcc (111) facets, whereas supported clusters stacked along the (111) bcc and (100) fcc planes. Structural transformation was induced by clusters containing greater numbers of atoms. Spread over the substrate enhanced interatomic energy, order substrates affect the epitaxial growth direction and increase the melting points of the supported clusters. This study can be used to predict the nature of fcc and bcc formation in Fe-Ni films.