Many studies have demonstrated microbial community response to individual cover crop species, but the effects of increasing cover crop diversity has received less attention. Moreover, there is increasing interest in conservation tillage strategies for cover crop termination and residue management. The objective of this study was to determine the relative influence of cover crop diversity and termination method on soil microbial community structure in an organic cropping system through the extraction of fatty acid methyl esters (FAMEs). A field experiment was conducted between 2009 and 2010 near Mead, NE where spring-sown mixtures of 0 (control), 2, or 8 cover crop species were included in a sunflower – soybean – corn crop rotation. Cover crops were planted in late-March, terminated in late-May using a field disk or undercutter and main crops were planted within one week. Three (2009) or four (2010) soil cores were taken to a depth of 20 cm in all experimental units at approximately 35 days following cover crop termination (early July). Canonical discriminant analysis of 2009 data indicated that 98% of the variation in microbial community structure was explained by cover crop termination method and residue management. Cover crop diversity was a much less important indicator of microbial community structure, as it only explained 1.2% of the total variation. However, microbial communities in cover-cropped soil were different from those in no-cover soils, which suggests that the presence of cover crops (regardless of the individual species in the community) was responsible for additional segregation of microbial community structure. Abundance of an arbuscular mycorrhizal fungi biomarker, C18:1(cis11), was greatest following cover crop termination with an undercutter, and lowest following termination with a field disk and in the no-cover control (p<0.10). Three bacterial biomarkers,C16:1(cis9), C17:1(cis9), C17:0, were greatest following cover crop termination with an undercutter and in the no-cover control, and lowest following termination with a field disk. These results suggest an increased abundance of both fungal and bacterial microbial groups following cover crop termination and residue management with a sweep plow undercutter.