A new system of soil quality estimation by means of microbial parameters is suggested for evaluation, quantification and monitoring of quality changes in arable automorphic soils of Moldova. The system is designed to overcome the shortcomings and limitations of individual microbial indicators and indices, and to produce clear and unequivocal information sufficient to measure the extent of degradation in an arable soil as compared to its virgin/undisturbed counterpart and to other arable soils. It also permits to detect the general direction of the changes in soil quality status at any particular point of time.