Abstract—A common denominator that affects the production areas is the dramatic loss of fertility and thus, the natural productive capacity of soils through a sustained process of erosion. The problem of soil loss was largely due to improper production practices, such as monoculture, chemical fertilizers, pesticides, intensive farming, genetically modified seeds, among others. Agroecological alternative that allows recovery of soils, compost making, and its quality depends of largely microbial diversity associated with it. The aim of the work focused on microbial characterization of different mixtures of agricultural waste in order to determine quality parameters. Through a randomized block design, six different mixes were evaluated in the village of Fusagasugá (Colombia). The OM, OC, macro and micronutrients chemical indicators were obtained from the soil laboratory at the University of Tolima, for microbial characterization macroscopic and microscopy techniques were used in the Laboratory of Microbiology of the University of Cundinamarca. Principal Component Analysis (PCA), a Canonical Correspondence Analysis (CCA) incorporating the Partial Least Squares (-Pls) was made. XLSTAT statistical package (2009.3.02) was used. The most important microorganisms were, Streptomyces, Arthrobacter, Aspergillus and Penicillium genera. Treatments that presented the best quality in relation to chemical and microbiological variables were mixtures containing double burden of animal, especially hens and pig manure.