At present, the range of starter cultures utilized in soybean fermented products is rather limited. In our prior research, it was discovered that Weissella confusa holds potential as a starter for soybean fermentation products. This study further probed into its entire genome and safety. Firstly, based on the safety assessment of the genome, we can gain a more profound understanding of gene functions, encompassing potential virulence factors, pathogenic traits, and glycosidase functions. The findings demonstrated that its gene function mainly concentrated on carbohydrate metabolism and amino acid metabolism, which further elaborated its capacity to ferment soybean products. Next, we verified that it did not possess genotoxicity through bacterial reversion mutation and in vitro mammalian cell micronucleus assays. Subsequently, the sensitivity of the antibiotic resistance gene to drugs was tested, and the results indicated that it was only resistant to vancomycin. Additionally, the determination results of extracellular enzymes were all negative, and the yield of biogenic amines was extremely low, with only weak α-hemolysis. Finally, in the acute toxicity test and subchronic toxicity test of mice, no adverse reactions associated with the tested substances were observed. In conclusion, it is demonstrated that Weissella confusa M1 is safe and can be utilized as a potential strain for food culture in the fermentation process.