To predict effects of climate change and possible feedbacks, it is crucial to understand the mechanisms behind pCO2 responses of biogeochemically relevant phytoplankton species. Previous experiments on the abundant N2-fixer Trichodesmium demonstrated strong pCO2 responses, which were attributed to an energy reallocation between its carbon and nitrogen acquisition. Pursuing this hypothesis, we manipulated the cellular energy budget by growing Trichodesmium erythraeum IMS101 under different pCO2 levels (180, 380, 980 and 1400 µatm) and nitrogen sources (N2 and NO3–). Subsequently, biomass production and the main energy-generating processes (photosynthesis and respiration) and energy-consuming processes (N2-fixation and carbon acquisition) were measured. While oxygen fluxes and chlorophyll fluorescence indicated that energy generation and its diurnal cycle was neither affected by pCO2 nor nitrogen source, cells differed in production rates and composition. Elevated pCO2 increased N2-fixation and organic carbon and nitrogen contents. The degree of stimulation was higher for nitrogenase activity than for cell contents, indicating a pCO2 effect on the transfer efficiency from N2 to biomass. pCO2-dependent changes in the diurnal cycle of N2-fixation correlated well with carbon affinities, confirming the interactions between nitrogen and carbon acquisition. Regarding effects of the nitrogen source, production rates were enhanced in NO3– grown cells, which we attribute to the higher N retention and lower ATP demand compared to N2-fixation. pCO2 effects on carbon affinity were less pronounced in NO3– users than N2-fixers. Our study illustrates the necessity to understand energy budgets and fluxes under different environmental conditions for explaining indirect effects of rising pCO2.