The application of novel bioorganic fertilizer (BIO) has been established as a weed biocontrol strategy, and reduce herbicides pollution and negatively effects on agricultural ecosystems. However, its long-term influences on soil bacterial communities are unknown. Here, 16 S rRNA sequencing to identify the changes that occur in soil bacterial community and enzyme under BIO treatments after five years in a field experiment. BIO application effectively controlled weeds, however no obvious differences between treatments were observed under BIO-50, BIO-100, BIO-200 and BIO-400 treatment.AnaeromyxobacterandClostridium_ sensu_ stricto_1were the two dominant genera among BIO-treated soil samples. The BIO-800 treatment had a slight influence on the species diversity index, which was more remarkable after five years. The seven significantly-different genera between BIO-800 treatment and untreated soils includedC._sensu_stricto_1,Syntrophorhabdus,Candidatus_Koribacter,Rhodanobacter,Bryobacter,Haliangium,Anaeromyxobacter. In addition, BIO application had different effects on soil enzymatic activities and chemical properties. The extractable P and pH saliency correlated withHaliangiumandC._Koribacter, andC._sensu_stricto_1observably correlated with exchangeable K, hydrolytic N and organic matter. Taken together, our data suggest that BIO application effectively controlled weeds and a slight influence on soil bacterial communities and enzymes. These findings expand our knowledge of the application of BIO as widely used as a sustainable weed control in rice paddy.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13568-023-01559-2.