PROBLEM TO BE SOLVED: To provide a fertilizer production system having such advantages as to make the best use of both anaerobic and aerobic reactions, be slight in offensive odor generation, and also be relatively high in reaction rate. SOLUTION: This fertilizer production system 1 which is equipped with a crusher 2 for organic leavings, disposer 3 for grinding crushed organic leavings, a microbial cell tank 4 for culturing microbial colonies, an activator tank 5 for containing a microorganism activator, and a fermentation tank 6 for fermenting a mixture liquor comprising organic leavings, microbial colonies, microorganism activator and water, has such a scheme that the discharge port of the crusher 2 is connected to the disposer 3, the discharge port of the activator tank 5 to the disposer 3 and the microbial cell tank 4, the fermentation tank 6 is divided into an aerating agitation tank 7 which may be overflown and an anaerobic reaction tank 8, and a 1st circuit 12 is provided so as to pass through the aerating agitation tank 7 and the disposer 3, while a 2nd circuit 14 so as to pass the anaerobic reaction tank 8 and the microbial cell tank 4.