Diazotrophic cyanobacteria fix both atmospheric carbon (C) and nitrogen (N) into biomass, but the two assimilation pathways are not compatible. Species like Anabaena sp. PCC 7120 physically separates C and N assimilation in different cell types. Even if separated, they are strongly intertwined, as N assimilation relies on the C skeletons and reducing power from photosynthesis, that in turn depends on N rich molecules as pigments and proteins. Whereas the two pathways have been extensively studied individually, here we investigate their interaction by analysing photosynthetic properties upon exposure to changes in light, CO2 and N availability, including the contribution of photosynthetic electron fluxes. Growth depended on the availability of both light and CO2, while the N2 fixation activity mainly on the C supply. Upon diazotrophic conditions, the total photosynthetic electron transport activity increased, with a modified contribution of different electron pathways. A mutant strain affected in the vehiculation of fixed N between cell types showed that the modulation of photosynthesis depended on the metabolic connection between assimilation pathways. Overall, data showed that the regulation of photosynthetic electron fluxes is a major component of the synergic metabolic relationship between C and N assimilation pathways upon dynamic environmental conditions.