Agricultural organic waste can be taken advantage of if one takes into account that it is a reusable source of nutrients and energy, reason why processes such as composting can improve its quality through aerobic decomposition. In an organic material composting process from coffee farms located in the Department of Cundinamarca (coffee pulp, bananas, manure and bovine manure) populations of bacteria, Treponema, and fungi were qualitatively and quantitatively characterized. The characterization of microbial populations was carried out through the application of techniques of serial dilution in selective culture ways and microscopy and macroscopia techniques. Micro-organisms of greatest importance found in pure substrates and their mixes were: for bacteria, the genera Pseudomonas and Bacillus; for Treponema Streptomyces and fungi, Aspergillus and Penicillium.