This study evaluated the effects of Lactiplantibacillus plantarum subsp. plantarum ZA3, Artemisia argyi and their combination, on the fermentation characteristics, microbial community, mycotoxins and crude flavonoids content of fermented soybean meal during fermentation (under anaerobic conditions) and aerobic exposure (under aerobic conditions). The results showed that ZA3, Artemisia argyi and ZA3+ Artemisia argyi groups had lower pH values and higher lactic acid concentrations compared with controls, and additives increased the abundance of Lactiplantibacillus and decreased those of Acetobacter and Enterobacter; in particular, Artemisia argyi and ZA3+ Artemisia argyi reduced the abundance of fungi, such as Aspergillus, Pichia, Fusarium, Cladosporium and Xeromyces. Meanwhile, the contents of mycotoxins were lower in treated groups, and even mycotoxins in the control were significantly reduced after 30 d (p < 0.05). Crude flavonoids that were correlated positively with Lactococcus and negatively with Bacillus, Aspergillus, Enterobacter and Kazachstania were significantly higher in the Artemisia argyi and ZA3+ Artemisia argyi groups (p < 0.05).