Purple blotch and anthracnose disease are the main diseases of shallots. The purpose of this study was to obtain an environmentally friendly technology for controlling purple blotch and anthracnose on shallots during the rainy season. The design used in this research was a split plot design with the main plots of local varieties of shallots (A) namely Sembrani, Bima Brebes and Maja Cipanas. As a sub-plot is the use of fungicides, namely chemical fungicides, chemical fungicides and bio-fungicides are used interchangeably and bio-fungicides are used routinely. The results of research conducted in the rainy season show that Sembrani variety had a significant effect on reducing the severity of purple blotch, anthracnose, and Stemphylium leaf blight disease compared with Bima Brebes and Maja Cipanas varieties. The use of chemical fungicides continuously is comparable to use of chemical fungicides and bio-fungicides which are carried out alternately in suppressing the severity of purple blotch, anthracnose and Stemphylium leaf blight diseases on shallots. Control by using chemical fungicides and bio-fungicides alternately that are can save the use of chemical fungicides by 50% thereby can protect the environment sustainability.