The great potential of whole-plant quinoa (WPQ) as a forage crop has been recognized in recent years. In this study, we investigated the effects of variety and harvest time on the fermentation characteristics, bacterial community, and hygienic quality of WPQ silage. Five varieties (Hongxin, Mengli1, SL577, SL2860, SL923) were grown across five separate experimental fields, with harvest occurring after 90 days (H1), 105 days (H2), or 120 days (H3). The samples were ensiled to evaluate their fermentation characteristics and bacterial composition. Hygienic quality was assessed using the Tax4fun2 and BugBase tools for potential pathogenicity and antimicrobial resistance prediction. The variety significantly influenced (P <
0.05) all fermentation variables (including pH, lactic acid, acetic acid, propionic acid, ethanol, and ammonia nitrogen), while harvest time affected pH and the contents of acetic acid, propionic acid, and NH