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Agriculture is going through a global crisis, productivity and sustainability are two factors, which farmers are challenging to produce more food, preserve the environment and the health of living beings. Developed and developing countries need to adopt new productive alternatives, which improve the quality of food, preserving the environment and the ecosystems. Actually, the abuse and misuse of chemical products has caused a series of problems such as contamination (soil and water) and pest resistance to active ingredients. Climate change and other transformations that agriculture is going through, generated decades ago the emergence of the industry of biological inputs, which are friendly products with the environment and human health. These products have characteristics and modes of action that help pest control with fewer risks than the use of pesticides. This review compiles the importance, use and applications of biological products based on beneficial fungi in Latin America, highlighting the project "Biocontrol for Sustainable Farming Systems" executed in Ecuador, funded by MFAT New Zeland, which has shown the efficiency of the use of microorganisms in the agriculture through the research results obtained during the execution of this Project. In addition, aspects related to quality control of bioproducts and regulations for their registration are also mentioned.