We report ab initio molecular dynamics simulations of vacuum-deposited iron-containing nitrogenated carbon. The study focuses on the effect of substrate temperature and presence or absence of hydrogen on the structure of the deposited films. It is found that carbon and nitrogen atoms in these structures behave similar to those in amorphous nitrogenated carbons. While some Fe atoms bond to the filled π orbitals of carbon−carbon bonds, others bond directly to their carbon and nitrogen neighbors. The Fe atoms increase the cross-linking of amorphous nitrogenated carbon networks. The density of states of the structures shows that there are Fe-related states just below the Fermi level, which might be important in electrocatalysis by using these films.