The soil microbial activity, biomass and structure were evaluated in an unamended (S) and organically amended soil treated with two commercial formulations of the herbicides chlorotoluron (Erturon®) and flufenacet plus diflufenican (Herold®) under field conditions. Soils were amended with spent mushroom substrate (SMS) or green compost (GC). Soil microbial dehydrogenase activity (DHA), biomass and structure determined by the phospholipid fatty acid (PLFA) profiles were recorded at 0, 45, 145, 229 and 339 days after herbicide treatment. The soil DHA values steadily decreased over time in the unamended soil treated with the herbicides, while microbial activity was constant in the amended soils. The amended soils recorded higher values of concentrations of PLFAs. Total soil microbial biomass decreased over time regardless of the organic amendment or the herbicide. Herbicide application sharply decreased the microbial population, with a significant modification of the microbial structure in the unamended soil. In contrast, no significant differences in microbial biomass and structure were detected in S + SMS and S + GC, untreated or treated with herbicides. The application of SMS and GC led to a significant shift in the soil microbial community regardless of the herbicides. The use of SMS and GC as organic amendments had a certain buffer effect on soil DHA and microbial biomass and structure after herbicide application due to the higher adsorption capacity of herbicides by the amended soils.