One method of controlling disease that is environmentally friendly is the use of plant-based pesticides also known as botanical pesticides. The use of botanical pesticides has proven to be effective in controlling several species of pests and plant diseases, because they contains active secondary metabolite compounds. These compounds affect pathogenic microorganisms, so it is feared will also affect antagonistic microorganisms. This research will find out the impact of the application of several botanical pesticides on shallots to microbial biodiversity. The study was conducted in Peat-lands, at South Kalimantan. Microbial identification was carried out at the Phytopathology Laboratory and the Laboratory of Biological Control of the Department of Pests and Plant Diseases, Lambung Mangkurat University, Banjarbaru. The results showed that the application of plant-based pesticides from Kepayang fruit extract and Galam leaf extract had an influence in decreasing the population of microorganisms, respectively by 80.44% and 75.26%. Chirinyuh were increased the population by 36.60%, as well as the control treatment, the population of microorganisms increased by 17.77%. Meanwhile the application of synthetic pesticide Dhitane M-45 reduced the population of microorganisms by 95.73%. Types of microbes found in the soil and onion rhizosphere are Pseudomonas flourescens, Bacillus sp., Fusarium sp., Aspergillus sp., Curvularia sp., Scopulariopsis sp., Stachybotrys bisbyi, and Penicillium sp.