AbstractParaquat is used as a harvest‐aid to desiccate green tissues for increasing harvest efficiency and maintaining seed quality. However, its application can cause significant crop damage and yield loss if applied too early. Limited information is available on determining the optimum time for applying paraquat. Therefore, the objectives of this study were to investigate the effects of the timing (critical stages of seed‐fill) of paraquat application on soybean seed yield, seed quality (germination, viability, hard‐seed, and seed damage), and seed composition. Field experiments were conducted in 2019 and 2020 at Stoneville, MS. Paraquat was applied at a rate of 0.56 kg a.i. ha–1 at growth stages R6 (full seed‐fill), R6.5 (pod cavities completely filled with seeds), or R7 (yellow color/beginning maturity). Cultivars P46A57BX and P48A60X were used. The results showed that the application of paraquat at R6 or R6.5 resulted in significant yield loss for both cultivars in both years, whereas application at R7 resulted in significant yield loss for P46A57BX in both years, but in only 1 yr for P48A60X. Seed germination and viability were significantly increased over the control in 2020 for both cultivars at all three application stages, but with mixed effects in 2019. No seed damage that would result in dockage was observed in any treatment, as seed damage for all treatments was below 2%. Application of paraquat at R6 resulted in significantly higher seed protein, oleic acid, raffinose, and stachyose but lower oil and sucrose. This research demonstrated that the harvest‐aid paraquat significantly reduced seed yield, increased seed protein, oleic acid, raffinose, and stachyose when applied before growth stage R7. Therefore, producers should use caution when applying paraquat for harvest efficiency before R7, as they will also likely reduce seed yield the earlier paraquat is applied.