Cyanobacteria have a strong potential for biofuel production due to their ability to accumulate large amounts of carbohydrates. Nitrogen (N) stress can be used to increase the content of carbohydrates in the biomass, but it is expected to reduce biomass productivity. Here, we characterized the biomass productivity, biomass composition as well as the transcriptome and proteome of the cyanobacterium Arthrospira sp. PCC 8005 cultured under N-limiting and N-replete conditions. N-limitation resulted in a large increase in the carbohydrate content of the biomass (from 14 to 74%) and a decrease in the protein content (from 37 to 10%). Transcriptomic and proteomic analysis confirmed that de novo protein synthesis was down-regulated and that proteins were degraded and partly converted into carbohydrates through gluconeogenesis, i.e. glycogen synthesis. The N from protein degradation was recycled through the TCA and GS-GOGAT cycles. Analyses of fatty acids indicated that no lipids were accumulated under N-limited conditions. N-limitation did not affect the biomass productivity of the culture up to five days after N was depleted from the culture medium, which might be explained by the fact that glycogen synthesis has a lower energy demand than protein synthesis.