Sclerotinia sclerotiorum is a soilborne pathogen of soybean that causes Sclerotinia stem rot, alternatively called white mold. Sclerotinia stem rot can cause significant yield losses under cool and wet environmental conditions. Two biofungicides, Coniothyrium minitans and Bacillus amyloliquefaciens, are currently available and labeled to limit or suppress S. sclerotiorum in soybean. These biofungicides can be applied in place of synthetic foliar fungicides to provide an alternative mode of action for the control of Sclerotinia stem rot. However, limited information is available regarding the efficacy of C. minitans and B. amyloliquefaciens as biocontrol agents of S. sclerotiorum in soybean. To assess the effectiveness of C. minitans and B. amyloliquefaciens as biocontrol agents of S. sclerotiorum dual culture and soil plate assays were conducted along with experiments in the growth chamber and field. Degradation of sclerotia following treatment with C. minitans in the soil plate assay confirmed that the primary mode of action is mycoparasitism. In the growth chamber, B. amyloliquefaciens at 14.03 liter/ha applied using the dip method significantly reduced Sclerotinia stem rot lesion length over the non-treated control and resulted in the lowest lesion area under the disease progress curve (lAUDPC). When B. amyloliquefaciens and C. minitans were applied in the field, no differences were observed between treatments for soybean moisture, test weight, or yield in Indiana.