In many developing countries around the world, the plan of producing sufficient biodiesel (EN 14214) to meet the mandate of 20% blending with the diesel fuel (EN 590) was unachievable particularly due to two main reasons - the unavailability of sufficient feedstock and lack of high yielding drought tolerant plant based feed-stocks. Also, the production of biodiesel from these plant based bio-degradable source such as vegetable oil competes with the farm land utilization meant for growing food crops. Hence, the development of algae based technologies for a sustainable yield of biodiesel is gaining widespread importance. Industrial waste water effluent and sewage sludge water provides the best source of nutrients for the cultivation of microalgae. It is an indisputable fact that the recoverable oil yield from this unicellular organism is higher than that of any other food crop. In spite of these efficacies, some of the performance influencing parameters such as cold flow and oxidative stability still remain unfavorable to be used for automotive application. The present investigation deals with the trans-esterification of fractionated monounsaturated fatty acid to produce biodiesel with better low temperature properties and higher resistance to oxidation. It was observed that the increasing trend of thermal and prompt NOx emissions was influenced by average Degree Of Unsaturation (DOU) in the trans-esterfied compound, as it increased the adiabatic flame temperature during combustion. Finally, a comparison was made between the fractionated and non-fractionated biodiesel to understand the profile of key emission influencing characteristics of fuel such as DOU, iodine value, chain length, cetane number and oxidative stability.