High value crops such as potato, onion, green bean, and strawberry are largely grown in intensive farming areas of Mediterranean countries. Yield and quality decline is a problem correlated to the progressive decline of soil organic matter (OM) content towards values unable to satisfy agricultural needs. Root rot disease, caused by a complex of fungal pathogens surviving on organic residues in soil, is one of the main factors of yield decline. Among many soil biological variables, root rot incidence can be a good bio-indicators of soil quality in intensive cropping systems. The control of root rot pathogens in soil is affected both by microbial activity and variability. In east Po Valley, Northern Italy, the total organic C content decline due to short rotations and intensive tillage has been drastically affected the microbial biomass content as well the variability of soil microbial communities. Moreover, another consequence has been the specialization of soil borne fungal pathogens toward the crops most frequently recurrent on soil. These cropping systems, where OM decline is a fertility-limiting factor, lead to the following research aspects: • the microbial components involved in soil suppressiveness toward root rot disease • how cropping practices can affect soil borne pathogens and microbial factors, • the relationship between soil biodiversity and soil health. Several experiments carried out so far both in field and lab conditions have shown that root rot disease incidence increases according with microbial biomass decrease in soil. The best method to increase OM in soil is to amend organic fertilizer with a high level of humic substances, whereas soil management practices that increase crop residues either into soil or on the soil surface, such as no tillage or green manuring, can increase soil borne pathogens impact on crops. Finally soil microbial diversity plays an important role in crop health.