Large amounts of sewage sludge are generated in urban wastewater treatment plants and used as fertilizer in agriculture due to its characteristics. They can contain contaminants such as heavy metals and pathogenic microorganisms. The objective of this research work is to study, in real conditions, the evolution of microbial concentration in agricultural soils fertilized by biologically treated sewage sludge. The sludge (6.25 tons Ha−1) was applied in two agricultural soils with different textures and crops. A microbiological (total coliforms, Escherichia coli, Staphylococcus aureus, Enterococcus sp., Pseudomonas sp., Salmonella sp. and total mesophylls) and physical-chemical characterization of the sludge, soils and irrigation water were carried out. The evolution of these parameters during sowing, growth and harvesting of crops was studied. Initially, sewage sludge had a higher concentration of microorganisms than soils. Irrigation water also contained microorganisms, fewer than sewage sludge amendment but not negligible. After amendment, there were no differences in the microbiological evolution in the two types of soil. In general, bacterial concentrations after crop harvest were lower than bacterial concentrations detected before sewage sludge amendment. Consequently, the application of sludge from water treatment processes did not worsen the microbiological quality of agricultural soil in this study at real conditions.