In this chapter, agricultural waste residue management by bio-organisms is discussed along with different types of decomposition processes. Tons of agricultural wastes are produced every year. These agricultural wastes create major environmental problems without effective means of management methods. There are many technologies being used for the decomposition, which mainly include anaerobic decomposition, compositing, fermentation, etc. All these decomposition processes depend upon the different soil-inhabiting microbes. These microbes are the key components of agri-residue decomposition process. Every step of decomposition requires different microbes. Various sets of catalytical enzymes are involved for the catabolic procedures of organic matter. By successive catabolic reactions, all the organic matters are mineralized into soil essential constituents, which will be the most effective sources of macro- and micronutrients for the soil fertility. Working efficiency of these microbes depends upon different parameters like moisture, temperature, pH, etc. The vitality and efficiency of microbes can be enhanced by using various inert carriers. If the efficiency of these soil microbes enhances by various factors, then the rate of decomposition could be enhanced to handle this ever-increasing problem of agriculture residue in near future.