The increasing CO2 emissions have a massive impact on the environment causing global warming due to the greenhouse effect. This leads to the effort of the society to minimize CO2 production as well as CO2 emissions mitigation by secondary measures to achieve sustainable and cleaner industrial production. Currently, research focuses on various methods for CO2 capture or mitigation from stationary industrial emission sources, such as waste-to-energy plants (WTEP), fossil fuel power plants, steel mills, cement plants, or refineries. One of the promising potential methods is the use of microalgae for biological CO2 fixation from flue gas through photosynthesis. With this vision, a vertical photobioreactor with elliptical tubes was developed, designed and implemented. This novel type of bioreactor using oval-shaped tubes, thus avoiding self-shading limitation, was used for experimental pilot-scale flue gas CO2 abatement verification. Flue gas composition was selected according to pollutants (CO, CO2, NO, SO2) on the outlet of the waste-to-energy plants. According to the suitable algae screening results, Chlorella pyrenoidosa Chick was used for cultivation. The biomass yield and CO2 fixation efficiency were experimentally obtained for optimal conditions and this new photobioreactor type. The results were compared to the available publications for Chlorella sp. and flue gas as the source of CO2. The best-achieved biomass productivities were 0.51 and 0.13 g L−1 d−1 with corresponding CO2 biofixation rates of 0.95 and 0.25 g L−1 D−1, respectively, for laboratory and pilot-scale. The results of this study allowed us to expand knowledge about high CO2 WTEP flu gas utilization as the carbon source for algae cultivation using novel PBR tubing. Also data about other minor flue gas pollutants (CO, NO, SO2) absorption in the cultivation medium contributes to an expansion of knowledge for algae cultivation using waste gas sources.