The present work focuses on the optimization of the energy conversion process and the use of algal resources for biodiesel production with ultrasound and microwave techniques in Oedogonium, Oscillatoria, Ulothrix, Chlorella, Cladophora, and Spirogyra for the first time. The fuel properties are investigated to optimize the efficiency of the newly emerging algal energy feedstock. The study indicates that the optimized microwave technique improves the lipid extraction efficiency in Oedogonium, Oscillatoria, Ulothrix, Chlorella, Cladophora, and Spirogyra (38.5, 34, 55, 48, 40, and 33%, respectively). Moreover, the ultrasonic technique was also effective in extracting more lipids from Oedogonium sp., Oscillatoria sp., Ulothrix sp., Chlorella, Cladophora sp., and Spirogyra sp. (32, 21, 51, 40, and 36%, respectively) than from controls, using an ultra-sonication power of 80 kHz with an 8-min extraction time. The fatty acid composition, especially the contents of C16:0 and C18:1, were also enhanced after the microwave and sonication pretreatments in algal species. Enhancement of the lipids extracted from algal species improved the cetane number, high heating value, cold filter plugging point, and oxidative stability as compared to controls. Our results indicate that the conversion of biofuels from algae could be increased by the ultrasound and microwave techniques, to develop an eco-green and sustainable environment.