Soil degradation caused by intensive land use (e.g., compaction, acidification, salinization, and continuous cropping obstacles) is a major constraint on the biological function and sustainable productivity of terrestrial agroecosystems. Microbial fertilizers (biofertilizers), which deploy beneficial functional microorganisms, are increasingly considered a promising biotic intervention to improve degraded soils by restoring microbial-driven ecosystem services. We quantitatively analyzed the intellectual evolution and spatiotemporal trajectories of 1,937 publications regarding biofertilizer-mediated soil improvement retrieved from the Web of Science Core Collection (2000-2025). The annual number of publications evolved through three phases: exploration period (2000-2006), stable development period (2007-2019), and rapid development period (2020-2025). The research is inherently interdisciplinary, centered on a “microorganism-soil-plant” framework, with India, China, and Pakistan emerging as the most productive countries. Co-citation network analysis reveals an intellectual evolution from classical soil analytics to modern applications in sustainable agronomy. Five interconnected thematic clusters emerged, representing the mechanistic chain from microbial function to ecosystem-level soil health. Research hotspots have shifted from basic methodology and functional mechanisms to sustainable agriculture integration. Future endeavors should integrate multi-omics insights with precision field applications to support the transition from empirical fertilization to microbial-based soil health management.