Food grade soybean production is a high value alternative to conventional soybean use. The production of natto, a fermented soyfood, requires soybean cultivars that consistently express specific quality traits over a range of growing environments. Therefore, it is necessary to evaluate genetic and environmental influence for natto quality traits to ensure consistent performance. A multi location experiment was conducted in 2006 and 2007 to address the influence of soybean cropping system (double crop vs. full season) and environmental factors on traits associated with natto quality. Two statistical models were used to analyze the effects of planting system and environment on agronomic traits such as yield, maturity, and seed size and natto quality traits such as water absorption, water loss after steaming, seed coat deficiency, and rate of water absorption. Genotype variation was significant for all traits, but genetic differences for water loss after steaming were minimal. Planting system significantly influenced all natto quality traits. Seed coat deficiency and rate of water absorption displayed the most differential response and double crop plantings produced superior characteristics. Genotype à environment interactions were significant for all traits, but they did not confound selecting superior natto cultivars. Significant environment and year effects indicate environmental sensitivity, but genotype rankings rarely changed. The results indicate that genotype was the most important factor controlling the natto quality traits tested. These results suggest breeding for superior natto cultivars is possible but environmental influence must be accounted for and multi environment testing is necessary for genotype natto quality evaluation.