The establishment of the incidence of different agricultural management practices on soil microbiological quality has become an issue of wide concern. This study was aimed to (i) determine the effect of different agricultural management practices (ecological, integrated, conventional, and conventional with the addition of pig slurry) on the microbial activity of a semi-arid soil at two different stages (cropped and fallow) and (ii) adapt an existing quantitative method to assess the microbiological soil quality in the different management systems. Several microbial and biochemical parameters, as well as two water-soluble carbon (C) fractions, were measured in the soil samples. Significant differences (P < 0.05) were found between the different agricultural management systems for most of the microbiological parameters during the cropped period. Factorial analysis indicated that adenosine triphosphate (ATP), microbial biomass C, diphenol oxidase activity, urease activity, and water-soluble carbohydrates had a high weight in factor 1. These parameters were selected to form part of the equation for calculating a microbiological quality index. During the cropped period, the ecological management yielded the highest score of the microbial quality index, whereas, during the fallow period, no differences were found among the index scores of the different agricultural management systems.