It is necessary to study soil health in terms of soil nutrient properties, soil microbial activity and diversity in conventionally and organically managed field for sustainable development in agriculture. In present investigation, different fermented organic inputs like farm yard manure, Beejamruth and Jeevamruth on soil nutrient parameters, mycoflora population and species diversity in Cotton field for three successive years. The soil amendments with organic inputs increased soil nutrient parameters like improvement in organic carbon (OC), Phosphorus (P), Potassium (K), water holding capacity (WHC) and positive decrease in soil pH and electrical conductivity over inorganic farming. The application of organic inputs enhances mycoflora colony forming unit (CFU) and more species diversity as compared to inorganic farming. From result it is confirmed that for maintenance of soil health i.e. soil fertility and microbial diversity, organic inputs is effective alternative to reduce the loss of over use of inorganic inputs towards sustainable and eco-friendly agricultural development for future.