Glyphosate applied POST can provide a high level of efficacy on many weed species in soybean, but delayed application beyond optimal weed growth stages might fail to fully protect yield potential. Further, we do not have a good understanding of the extent to which delayed glyphosate application and its associated yield loss is occurring on-farm. Our goal was to characterize on-farm weed communities in glyphosate-resistant soybean just prior to glyphosate application and estimate potential yield loss associated with early-season soybean-weed competition. In field surveys conducted across 64 site-yr in southern Wisconsin in 2008 and 2009, common lambsquarters, velvetleaf, dandelion, Polygonum spp., and Amaranthus spp. were the five most abundant broadleaf weed species across site-years, present in 92, 69, 64, 42, and 50% of all fields, respectively, at average densities of 14, 5, 5, 14, and 10 plants m−2, respectively. Average height of these species was 21 cm or less at or near the time of glyphosate application. Grass and sedge species occurred in 95% of fields at an average density of 41 plants m−2 and height of 21 cm. The mean and median values of total weed density across site-years were 101 and 41 plants m−2, with heights of 19 and 17 cm, respectively. Recommended height for treatment is 15 cm. Glyphosate application occurred on average at V3 to V4 soybean growth stage, which is later than V2 soybean typically targeted to protect yield. Average yield loss predicted by WeedSOFT® was 5% with a mean economic loss of $47 ha−1. Predicted yield loss was greater than 5% on one-fourth of the site-years, all of which were treated at V4 soybean or later. The maximum predicted yield loss was 27%. These results suggest that glyphosate was applied at weed height and soybean growth stages that were greater than optimal to protect yield in many fields across southern Wisconsin. A soil-residual herbicide applied PRE, or a more timely POST application of glyphosate would alleviate the majority of these losses.