In response to concerns from certified organic producers who were experiencing significant market losses due to seed staining of soybean [Glycine max (L.) Merr.], we evaluated alternative ways to manage bean leaf beetles [Cerotoma trifurcata (Forster)] (Coleoptera: Chrysomelidae), a known vector for the seed-staining bean pod mottle virus (BPMV). From 2000 through 2006, organic-compliant treatments, including insecticidal and soil fertility products in use by organic farmers, were compared in on-farm and experiment-station trials. Two soybean varieties, Northrup-King 2412 (NK2412) and Pioneer Brand 9305 (P9305), also were evaluated for bean leaf beetle populations. Overall, the NK2412 variety hosted fewer beetles although there was not a significant yield effect. None of the organic-compliant treatments provided measurable control of bean leaf beetle populations, nor did they affect beneficial insect populations. Organic soybean yields ranged from 1.8 to 3.7 Mg ha−1 across all years with no effect from treatments. Producers are encouraged to select soybean varieties based on insect pest response and to monitor bean leaf beetle populations to determine the effectiveness of this strategy in organic systems.