Rising level of pollution and extreme rate of depletion of fossil fuels has become a major issue in today's world which requires immediate measures for its prevention. Biodiesel is the potential answer to this threat to environment as being an extremely promising fuel given its adaptability of usage in currently existing engine modules. Out of various oil sources for biodiesel production (Jatropha, Pongamia, Neem, Mahua) Cotton seed oil is one of the prominent source for biodiesel production in India. The aim of this study to enhance the fuel quality of cotton seed biodiesel so that it can be used as an alternative fuel. Viscosity is an important indicator of progression of oxidation in biodiesel to be used in an engine. Viscosity and flash point of biodiesel is optimized with the help of anti-oxidant (pyrogallol) and by governing the adverse effects of oxidizing agent as metal contaminants of aluminium. The experimental investigation reveals that Cotton seed biodiesel (CB 20) with metal contamination there is decrease of 21.03% in brake thermal efficiency (BTE) and without metal contaminants there is decline of 11% was found as compared to diesel while brake specific fuel consumption (BSFC), was increased by 25.84% for CB 20 with metal contaminants and for CB 20 (without metal contaminants) there is increase in 10.73% as compared to diesel. There was a significant reduction in exhaust emissions including carbon monoxide (CO) and (CO 2) as for CB 20 value reduction for CO 2 was 41.35% and 38.27% for samples with and without metal contaminants. However, a 15.84% and 11.2% increase in oxides of nitrogen (NO x) emission was experienced for biodiesel mixtures for CB 20 with and without metal contaminants respectively as compared to diesel.