For agricultural reuse, the disinfection treatment must be efficient to inactivate the resistant pathogens and must not generate harmful byproducts for the soil and crop production. Thus, the aim of this work was to evaluate the possible impacts caused by the irrigation with wastewater disinfected with sodium hypochlorite, peracetic acid, ultraviolet radiation, or the oxidation process UV radiation combined with hydrogen peroxide over soil physicochemical properties and microbial community composition, as well as over the wheat crop yield in the short term. A pot essay was performed in a greenhouse, and at the end the main alterations observed in soil physicochemical properties were due to water type, not to the disinfection treatments. The crop yield was influenced by the water type, but not by the disinfectant treatments. Irrigation with wastewater improved almost 5 times the wheat grains yield, compared with freshwater. Wastewater irrigation increased the abundance of families involved in organic matter degradation and nitrogen cycle, and some pathogenic bacteria. Among the disinfectant treatments, the UV disinfection played an important role in shaping soil bacterial community structure.