Global warming caused by greenhouse gas emission is a major threat in recent times. Carbon dioxide (CO2) is a major source of greenhouse gas emission from CI engine. The present study aims to investigate the effect of pre-combustion, oxygenate and post-combustion system with biofuel blends in single cylinder CI engine on CO2 emission. All the experiments were conducted in a single cylinder CI engine with 5.2 kW rated power at 1500 rpm at 50% and 100% load. Diesel is replaced with Karanja oil methyl ester (KOME) and both are taken as baseline data. Low carbon biofuel namely orange oil (ORG) was blended on an equal volume basis with KOME and tested. Zeolite based post-combustion capture system (ZPCS) and fuel ionization filter (FIF) as pre-combustion capture system was tested along with 20% methanol (M) blend with KOME-ORG. FIF electrochemically ionizes the fuel molecules and aids in quick dispersion of the ions for improved combustion. Hydrocarbon based biofuels are converted to carbon, hydrogen and oxygen ions, where hydrogen takes part in combustion and oxygen enhances the combustion process. At 100% load, CO2 emission for KOME-ORG + M20 + FIF + ZPCS is 68% less compared to KOME. The combination also reduces NO and smoke by 48% and 51% compared to KOME at 100% load. The combined effect of FIF, ZPCS and methanol aided in the simultaneous reduction of NO, smoke and CO2 emission.