The recycling of nitrogen is essential for all organisms on earth and microbial communities play crucial roles in the nitrogen biogeochemical cycle. Constant anthropogenic alterations (both positive and negative) and changing environmental conditions (such as climate change and ocean acidification) have profound effects on the nitrogen cycle. In order to fully elucidate the nitrogen cycle, adequately address the consequences of environmental perturbations and mediate nitrogen pollution, nitrogen transformations need to be thoroughly investigated and ideally, modelled. Systems approaches, typically analysing DNA, RNA, proteins and metabolites together with the corresponding metadata prevailing in the ecosystem under study, ultimately aim at developing models to characterize the ecosystem attributes and predict the consequences of changes in environmental conditions in silico. Therefore, systems approaches hold a lot of potential when applied to the nitrogen cycle. In such context, metaproteomics, defined as the analysis of the proteins collectively expressed by all the organisms present in an ecosystem, becomes a crucial requirement. In this chapter we will discuss how metaproteomics, typically combined with other 'omics' technologies, has advanced our understanding of the nitrogen cycle in different environments. We will also discuss proteomic studies of relevant microbial isolates, as well the application of isotope labelling proteomics to the nitrogen cycle.