<p>Biofertilizers are key tools for sustainable agriculture and soil health Maintenance, yet their specific effects on soil functions and microbiota remain unclear. In order to address this, we aimed to evaluate how a biofertilizer alters soil microbial communities, physicochemical properties, and functions after 18&#xa0;months of periodical use in a kaki monoculture. We found that the biofertilizer indirectly reshaped microbial community structure—especially bacterial diversity—likely through interactions with the native microbiome. Functional changes included increased microbial biomass, nitrogen mineralization, and dehydrogenase activity, with reduced acid phosphatase activity. The composition of bacterial and fungal communities exhibited significant differences between biofertilizer-treated soils and control soils across most evaluated taxonomic levels. Biodiversity was altered with biofertilizer application in bacterial communities, while fungal communities were less affected. Microbial co-occurrence networks differed between the two soil treatments, although a few patterns were consistent among treated and control soils. A novel contribution of this work is the integration of co-occurrence network analysis with microbial functional traits, revealing that core microbial networks linked to nitrogen and phosphate cycling persist despite disturbance. These findings highlight the role of microbial biodiversity and community assembly in sustaining soil functions under biofertilizer application.</p>