• WCO biodiesel properties and fatty acid profile depend on the source and heating cycles. • Repeated heating caused reduced unsaturated and increased short-chain compounds. • Repeated heating resulted in increased density, viscosity, and calorific value. • Repeated heating decreased BTE, smoke opacity, and increased HC and NO x . • Coconut-based biodiesels showed better engine performance and emission comparatively. Using cooking oil multiple times is a common practice to reduce the food preparation cost, which causes many health issues, also simply throwing it away will cause environmental pollution. Hence, converting waste cooking oil into biodiesel is a solution to waste management with energy production. This study analyzed the effect of the number of heating cycles of coconut, sunflower, and palm oils on the fatty acid configuration and properties of biodiesel produced from them. A reduction in unsaturated compounds, increase in short-chain components, increase of 0.266%, 0.365%, and 0.347% in density, increase of 5.06%, 12.29%, and 8.83% in kinematic viscosity, increase of 0.266%, 0.365%, and 0.347% in calorific value are observed with five repeated heating of coconut, sunflower, and palm oils, respectively. Performance, combustion, and emission analysis of a diesel engine fueled with B20 blends of biodiesels showed a decrease of 0.27 %, 0.28 %, and 0.52 % in brake thermal efficiency, an increase of 2.44 J/deg, 3.43 J/deg, and 2.74 J/deg in peak heat release rate, an increase of 7 ppm, 65 ppm, and 60 ppm in NO x emission, and decrease of 4.5 %, 2.8 %, and 1 % in smoke opacity with five repeated heating of coconut, sunflower, and palm oils, respectively. Even though the brake thermal efficiency and emissions (except NO x ) were found decreased for all biodiesel blends compared to diesel, coconut-based biodiesels were found to be the best alternative among all the biodiesels with reduced HC, NO x , and smoke as compared to diesel.