<p>Chemical fertilizers have substantially increased crop yields but have also contributed to significant environmental challenges, including soil and water contamination and the emergence of human health issues. As a more sustainable alternative, biofertilizers—comprising beneficial microorganisms such as bacteria—have been promoted as eco-friendly solutions. However, their use may pose risks to soil microbial communities and biodiversity under certain conditions. For instance, horizontal gene transfer among bacteria can convert non-pathogenic strains into pathogenic ones. Additionally, the introduction of microbial inoculants may outcompete native microbial species, potentially disrupting soil microbial balance and impairing ecosystem functioning. The long-term effects of biofertilizers on nutrient cycling and soil biodiversity remain insufficiently studied. To mitigate these risks, it is crucial to establish rigorous production standards, prioritize native microbial strains, continuously monitor soil microbial dynamics, and implement comprehensive regulatory frameworks. Therefore, the adoption of biofertilizers in agricultural practices should be approached cautiously and guided by evidence-based regulations.</p>