Soil fertility amendments, including composted cotton-gin trash, swine manure, a rye-vetch green manure, or synthetic fertilizers, were applied to subplots and tillage on bare soil; or tillage followed by surface mulch with wheat straw were applied to main plots to determine the effect on the incidence of southern blight caused by Sclerotium rolfsii, yield of processing tomato, and soil microbial communities. The amendment-tillage interaction was significant in 1997 and disease incidence was 67% in tilled bare soil receiving synthetic fertilizers; whereas disease incidence was 3, 12, and 16% in surface-mulched plots amended with a composted cotton-gin trash, swine manure, or a rye-vetch green manure. The amendment effect was significant in 1998, and disease incidence was 61% in plots receiving synthetic fertilizer and was 23, 44, and 53% in plots receiving cotton-gin trash, swine manure, or rye-vetch green manure, respectively. In 1997, yields were highest in tilled surface-mulched plots amended with synthetic fertilizers, cotton-gin trash, or swine manure, respectively. In 1998, yields were low in all plots and there were no significant differences in yield due to treatment. Propagule densities of antagonistic soil fungi in the genus Trichoderma were highest in soils amended with composted cotton-gin trash or swine manure in both years. Propagule densities of fluorescent pseudomonads in soil were higher in plots amended with organic amendments than with synthetic fertilizers in both years. Propagules densities of enteric bacteria were elevated in soils amended with raw swine manure biosolids in both years. Our research indicates that some organic amendments, such as cotton-gin trash, reduced the incidence of southern blight in processing tomato and also enhanced populations of beneficial soil microbes.