Flue gas emissions are the waste gases produced during the combustion of fuel in industrial processes, which are released into the atmosphere. These identical processes also produce a significant amount of wastewater that is released into the environment. The current investigation aims to assess the viability of simultaneously mitigating flue gas emissions and remediating wastewater in a bubble column bioreactor utilizing bacterial consortia. A comparative study was done on different growth media prepared using wastewater. The highest biomass yield of 3.66 g L−1 was achieved with the highest removal efficiencies of 89.80, 77.30, and 80.77% for CO2, SO2, and NO, respectively. The study investigated pH, salinity, dissolved oxygen, and biochemical and chemical oxygen demand to assess their influence on the process. The nutrient balance validated the ability of bacteria to utilize compounds in flue gas and wastewater for biomass production. The Fourier Transform–Infrared Spectrometry (FT–IR) and Gas Chromatography–Mass Spectrometry (GC–MS) analyses detected commercial-use long-chain hydrocarbons, fatty alcohols, carboxylic acids, and esters in the biomass samples. The nuclear magnetic resonance (NMR) metabolomics detected the potential mechanism pathways followed by the bacteria for mitigation. The techno-economic assessment determined a feasible total capital investment of 245.74$ to operate the reactor for 288 h. The bioreactor’s practicability was determined by mass transfer and thermodynamics assessment. Therefore, this study introduces a novel approach that utilizes bacteria and a bioreactor to mitigate flue gas and remediate wastewater.