Organic farming is an alternate method of agriculture, in which the farmers use natural processes, avoiding synthetic inputs. After the Green revolution, conventional agriculture had been widely accepted in the country. It helped the country produce sufficient food to feed the people. It also promoted exports of food grains worldwide. Conventional agriculture methods increased the total production in agriculture and also increased the income of farmers. In this method of agriculture, chemicals and pesticides are widely used, which can sometimes create negative effects on the human body and the environment. Organic farming creates good impacts by using Bio fertilizers, on human health with zero negative impacts on the environment. Though the method is good and has opportunity in future, but the field of Bio fertilizers has many challenges. Organic farming is facing various kind of Issues. The paper discusses about the challenges and prospects in the field of organic farming specially related to Bio fertilizers in India