Farming practices can have profound affects on different soil properties, including various physical, chemical and biological characteristics. The influences of different farm management strategies on soil-borne disease development, plant vigor and microbial community structure were studied. Four organically acceptable transitional cropping strategies with and without compost amendments were considered: mixed hay, field vegetables, high tunnel vegetables and tilled fallowing. Differences in disease suppressiveness and plant vigor were assayed using edamame soybeans (cv. Sayamusume). The effects of compost addition on soil characteristics varied with transition strategy, with the greatest effects being observed in the soils coming from the mixed hay and high tunnel treatments. Under low disease pressure conditions compost additions uniformly resulted in an increase in plant vigor. But, under high disease pressure disease severity increased with the addition of the compost amendments, and the mixed hay treatment was much less conducive to disease development. Such differences in plant health are being associated with treatment-induced variations in rhizosphere microbial community structure. A combination of culture-dependent and culture-independent approaches are being used to identify microbial populations whose abundance varies with farm management practices. Such correlations are expected to lead to the identification of novel populations of plant health promoting rhizobacteria. On edamame soybeans, compost amendments led to higher rhizosphere colonization rates of various Pseudomonas spp. under all cropping strategies, indicating a general role for such populations in promoting plant health. Understanding the effects of field management on plant health, pathogen populations and pathogen antagonists will be useful for designing cropping strategies that reduce disease development in the field.