A continuous flow system for production of bio-fuels using microbial cultures is provided. The present invention does not utilize batch type production, but follows a continuous flow protocol that eliminates much downtime inherent in conventional bio-fuel production systems while greatly reducing space and equipment requirements. Production is enhanced via controlled program of aeration for microbial growth and anaerobic conditions to ensure fermentation efficiency. As the system becomes more tolerant of alcohol content, efficiency increases. Feedstocks include, but are not limited to, material normally discarded from food production facilities including drink syrups, juices or waste water from corn or sugar processing plants.