This study uses the first and second laws of thermodynamics to investigate the effect of oxygenated fuels on the quality and quantity of energy in a turbo-charged, common-rail sixcylinder diesel engine. This work was performed using a range of fuel oxygen content based on diesel, waste cooking biodiesel, and a triacetin. The experimental engine performance and emission data was collected at 12 engine operating modes. Energy and exergy parameters were calculated, and results showed that the use of oxygenated fuels can improve the thermal efficiency leading to lower exhaust energy loss. Waste cooking biodiesel (B100) exhibited the lowest exhaust loss fraction and highest thermal efficiency (up to 6% higher than diesel). Considering the exergy analysis, lower exhaust temperatures obtained with oxygenated fuels resulted in lower exhaust exergy loss (down to 80%) and higher exergetic efficiency (up to 10%). Since the investigated fuels were oxygenated, this study used the oxygen ratio (OR) instead of the equivalence ratio to provide a better understanding of the concept. The OR has increased with decreasing engine load and increasing engine speed. Increasing the OR decreased the fuel exergy, exhaust exergy and destruction efficiency. With the use of B100, there was a very high exergy destruction (up to 55%), which was seen to decrease with the addition of triacetin (down to 29%).