Cultural practices such as organic amendments, rotations, and use of biological control organisms are regularly investigated for their effects on controlling plant diseases but their effects on soil microbial populations are often unexplored. In this study, three different sustainable disease management practices, use of compost amendment, biocontrol organisms, and a potentially disease-suppressive rotation, were established in potato field trials at two sites under different management regimes and histories, and evaluated over three potato cropping seasons for their effects on soil microbial communities. Specific management factors assessed included the presence or absence of a conifer-based compost amendment, addition of one of three different biocontrol organisms (Trichoderma virens, Bacillus subtilis, and Rhizoctonia solani isolate Rhs1A1), and a Brassica napus (rapeseed) green manure rotation crop preceding potato, and treatments were assessed in all factorial combinations. The two farm sites represented organic and conventional potato production practices in Aroostook County, Maine. Compost amendment and rapeseed rotation had the greatest impacts on soil microbial communities, with both treatments increasing total populations of culturable bacteria at both sites over the course of the study, as well as causing detectable shifts in soil microbial community characteristics as determined by sole carbon-source substrate utilization and fatty acid methyl ester (FAME) profiles. Compost amendment generally led to increased utilization of complex substrates and increased levels of Gram-positive bacteria and fungi, and compost effects were more pronounced at the conventional site. Rapeseed rotation often resulted in somewhat different effects at the two different sites. Consistent overall effects were observed with the biocontrol amendments Rhs1A1 and T. virens, including increased microbial activity and bacterial populations. Combined effects of multiple treatments were greater than those of individual treatments and were generally additive. These results indicate that each treatment factor had significant and specific effects on soil microbial communities, and that combined effects tended to be complementary, suggesting the potential of combining multiple compatible management practices and their associated changes in soil microbial communities.