Organic fertilizers manufacture has currently taken a great importance due to the need to add organic matter to improve soil conditions, and inorganic nutrient sources for plants. The quality of the AO F is measured by different variables: chemical composition, enzymatic activity, mineralization and humus-making processes, and microbial populations, among others; the preparation shows oxic and anoxic environments with different moisture percentage, pH and temperature, which means that microbial populations correspond to these environments as well as to the raw materials (from both organic and inorganic origin) included in the process. Consequently, new molecules are produced by these materials fermentation. These environments get altered due to the turn-overs needed to homogenize the material so the abiotic conditions for the populations change. These populations were measured in the nucleus and the crust, in three different strata. The quantification of nitrogen-fixers microorganisms (MFN), phosphorus solvent (SPS) and sulfate reducer (MSR), both during and at the end of the process, allowed to determine that MFN show the highest populations while the other populations evaluated are not relevant.