The long-term performance of a tubular photobioreactor interconnected to a gas absorption column for the abatement of CO2 from biogas and flue-gas was investigated. Additionally, a novel nitrogen feast-famine regime was implemented during the flue-gas feeding stage in order to promote the continuous storage of highly-energetic compounds. Results showed effective CO2 (~98%) and H2S (~99%) removals from synthetic biogas, supported by the high photosynthetic activity of microalgae which resulted in an alkaline pH (~10). In addition, CO2 removals of 99 and 91% were observed during the flue-gas operation depending on the nutrients source: mineral salt medium and digestate, respectively. A biomass productivity of ~8 g m−2 d−1 was obtained during both stages, with a complete nitrogen and carbon recovery from the cultivation broth. Moreover, the strategy of feeding nutrients during the dark period promoted the continuous accumulation of carbohydrates, their concentration increasing from 22% under normal nutrition up to 37% during the feast-famine cycle. This represents a productivity of ~3 g-carbohydrates m−2 d−1, which can be further valorized to contribute to the economic sustainability of the photosynthetic CO2 removal process.