Abstract:[Objective] Ageratina adenophora, a most harmful invasive plant in China, contains many toxicants to animals, plants and microbes. To understand the toxicity of its decomposed materials by microbial inoculants to soil microbes and plants is beneficial to produce organic fertilizer (OF).[Methods] A field experiment, including the control (CK), sole chemical fertilizer (CF), pure OF, and combination of CF and OF (CF+OF), was conducted to study the effect of OF on soil bacteria, and yield and quality of pepper.[Results] Providing soil with OF resulted in higher microbial biomass than CF. Both OF and CF+OF increased bacterial community indexes in contrast to CF that increased microbial dominant index in soils. Actinobacteria and Proteobacteria accounted for more than 50% of the total bacteria in each soil examined. Among top 20 predominant bacteria, 7 were ubiquitous in all studied soils and 6 to 8 were unique in each soil. Furthermore, there were higher nutrient concentrations in the soil supplied with CF in early fruit stage, whereas that with CF+OF contained higher available phosphorus and rapidly available potassium than CF, and alkaline hydrolyzed nitrogen was similar in late fruit period. Pepper plants fertilized with CF+OF absorbed more nitrogen, phosphorus, and potassium, produced 14.4% more fruits than CF and improved pepper fruit quality.[Conclusion] OF application enriched soil bacterial groups, increased soil microbial biomass, and pepper fruit yield and quality. Organic fertilizer made from A. adenophora improves soils for pepper plants.