The individual steps of catalysis within the biogeochemical nitrogen cycle—and in particular within the denitrification pathway—occur on both sides of the cytoplasmic membrane that, in the process, gets energised through the formation of a proton motive force. In several instances, reaction intermediates must pass the hydrophobic barrier of the membrane. While this is unproblematic for gaseous compounds such as nitric oxide, N2O or N2, the three ionic species NO3−, NO2− and NH4+ require specific and distinct membrane transport systems in order to convey substrate translocation. Several types of transporters and a broad variety of transport mechanisms are at work, ranging from primary active transport driven by ATP hydrolysis via secondary active proton symport to passive channelling. An overview of the membrane transport proteins of the nitrogen cycle thus constitutes a broad survey of the existing mechanisms and modes of protein-mediated ion translocation across lipid bilayers.