The energy conversion efficiency of the pretreated algae bloom biomass with acid-domesticated hydrogenogens was remarkably increased to 47.0% by cogenerating 256.7 mL/g-TVS hydrogen and 253.5 mL/g-TVS methane in a three-stage process (dark-fermentation, photofermentation, and methanogenesis). Compared with steam heating with dilute acid, microwave heating with dilute acid, which resulted in higher hydrolysis efficiency, degraded algal cells into smaller fragments. Hydrogenogens were domesticated with acids to improve their adaptation to fermentative environments and increase hydrogen production. Further studies should be conducted to determine the effects of algal toxins on the cogeneration of fermentative hydrogen and methane.