Ammonia (NH3) synthesis is an essential yet energy-demanding industrial process. Hence, there is a need to develop NH3 synthesis catalysts that are highly active under milder conditions. Metal nitrides are promising candidates, with the η-carbide Co3Mo3N having been found to be more active than the industrial Fe-based catalyst. The isostructural Fe3Mo3N catalyst has also been identified as highly active for NH3 synthesis. In the present work, we investigate the catalytic ammonia synthesis mechanisms in Fe3Mo3N, which we compare and contrast with the previously studied Co3Mo3N. We apply plane-wave density functional theory (DFT) to investigate surface N vacancy formation in Fe3Mo3N, and two distinct ammonia synthesis mechanisms. The calculations reveal that whilst N vacancy formation on Fe3Mo3N is more thermodynamically demanding than for Co3Mo3N, the formation energies are comparable, suggesting that surface lattice N vacancies in Fe3Mo3N could facilitate NH3 synthesis. N2 activation was found to be enhanced on Fe3Mo3N compared to Co3Mo3N, for adsorption both at and adjacent to the vacancy. The calculated activation barriers suggest that, as for Co3Mo3N, the associative Mars van Krevelen mechanism affords a much less energy-demanding pathway for ammonia synthesis, especially for initial hydrogenation processes.