Nitrogenase is the only known enzyme that catalyzes the reduction of atmospheric dinitrogen into ammonia. The most common form of nitrogenase is composed of two proteins: the catalytic component termed the molybdenum-iron protein (MoFeP) and the ATP-dependent reductase component termed the iron protein (FeP).  Previous studies have shown that FeP or MoFeP component in a given diazotrophic organism is often functionally compatible with their partner from a different diazotroph. However, such heterologous nitrogenase systems often exhibit reduced catalytic activities, and the underlying causes of this diminished efficiency remain unclear. Structural and biochemical characterizations of heterologous nitrogenase complexes offer a valuable approach to elucidate the interactions between MoFeP and FeP. In this study, we present cryo-electron microscopy (cryoEM) structures of the FeP-MoFeP complex from Gluconacetobacter diazotrophicus, as well as two heterologous nitrogenase complexes formed between G. diazotrophicus and Azotobacter vinelandii species. Despite the distinct physiological characteristics of G. diazotrophicus (an endophytic microaerophile) and A. vinelandii (a free-living obligate aerobe), we find that their nitrogenase components are compatible with one another and their complexes can support nitrogen fixation. The two heterologous complexes exhibit high structural similarity, including conserved FeP docking geometries, nearly identical distances between their iron–sulfur clusters, and similar conformations of key catalytic residues. Nonetheless, these heterologous complexes display approximately 60% of the catalytic activity observed in homologous systems, while consuming ATP at comparable rates. These findings demonstrate that both homologous and heterologous nitrogenase complexes can adopt the proper complexation geometry to enable ATP-coupled electron transfer. Moreover, our results suggest that non-conserved regions of nitrogenase play a significant role in modulating protein-protein interactions and catalytic efficiency.