A complex treatment of agricultural waste including the following major steps: anaerobic fermentation of suitable waste, cogeneration of the obtained biogas and growth of microalgae consuming the CO(2) from biogas and flue gas was verified under field conditions in a pilot-scale photobioreactor. The growth kinetics of microalgae Chlorella sp. consuming mixture of air and carbon dioxide (2% (v/v) of CO(2)), or flue gas (8-10% (v/v) of CO(2)) was investigated. The results obtained in the pilot photobioreactor were compared with results previously measured in laboratory photobioreactors. The field tests were performed in a pilot-scale outdoor solar-bubbled photobioreactor located at a biogas station. The pilot-scale photobioreactor was in the shape of a flat and narrow vertical prism with a volume of 300 L. The microalgae growth rates were correlated with empirical formulas. Laboratory analyses of the produced microalgae confirmed that it meets the strict EU criteria for relevant contaminants level in foodstuffs. Utilization of flue gases from cogeneration therefore was not found to be detrimental to the quality of microalgal biomass, and may be used in these types of bioreactors.