Red Monascus pigments, azaphilone alkaloids from Monascus sp., have been utilized as natural food colorant more than 1000 years in China. Other azaphilones are being developed as alternative sources of natural pigments. Rotiorin or rotiorin alkaloids are always only achieved by solid-state fermentation or liquid culture without stirring due to carbon/nitrogen metabolism affecting pH of the culture medium and the pH environment further affecting the rotiorin stability/reactivity. In the present work, based on the biocompatible reaction of rotiorin with primary amines using phosphate as catalyst, biosynthesis of rotiorin and chemical conversion of rotiorin into its alkaloids were designed as cascade reactions where rotiorin was prevented from degradation and rotiorin alkaloids were accumulated directly by submerged culture of P. sclerotiorum. This is a facile strategy for direct production of rotiorin alkaloids, which provides the precondition for exploiting rotiorin alkaloids as an alternative source of natural colorant.