The global demand for protein led to the increase of animal production in the world and, mainly, in Brazil. As a consequence, there was an increase in the amount of waste produced, and the need to seek alternatives for its sustainable use. Microbial indicators and multivariate tools can assist in the proper measurement of the impact of the use of this waste on the soil. This study aimed to: 1) measure the effect of the application of organic fertilizers of animal origin in the no-tillage system on soil microbial attributes and its relationship with maize yield; 2) evaluate the potential of separation/discrimination of the different sources of organic fertilizers based on yield and soil microbial and chemical-physical attributes, using multivariate tools. Treatments consisted of annual application of: poultry manure (PM), liquid swine manure (LSM), poultry manure compost (PMC), swine manure compost (SMC), cattle manure compost (CMC) and control (C), without fertilization. Organic fertilizers promoted higher values of microbial biomass (MB) and MBC:TOC ratio in treatments CMC, SMC and PM in the first sampling season (E1), followed by PM, LSM and PMC in the second sampling period (E2). The data show that PM promoted microbial growth in both seasons, with higher metabolic efficiency increasing maize yield by 30% in relation to the treatment with the second highest production, PMC. Multivariate analysis techniques prove to be important tools to study soil quality indicators in systems which use organic fertilizers.