Fertilization treatments caused long-term changes in some biological parameters such as: MicroRespTM parameters, citrate utilization, total substrate-induced respiration value, and the ratio of utilization of amino acids and sugars. The rate of AMF colonization responded mainly to the plant nutrition status and the plant requirements, suggesting a plant-mediated effect in the case of mycorrhiza. Mineral nitrogen fertilization and soil acidification were found to be the main factors affecting the catabolic activity of soil microbiota, while AMF colonization responded to the balance of plant nutrition.