Organic–Inorganic Combined Application: A Review of Long-Term Experimental Insights and Pathway to Sustainable Sugarcane Production

This review synthesizes evidence from long-term field experiments, meta-analyses, and high-throughput sequencing studies on combined organic–inorganic fertilization, with a focus on sustainable sugarcane production in Yunnan, China. Prolonged use of inorganic fertilizers degrades soils through acidification, loss of organic matter, and reduced microbial diversity. Integrated nutrient management sustains crop productivity while maintaining soil health, outperforming inorganic-only applications. Organic amendments, including farmyard manure and sugarcane by-products such as pressmud, vinasse, and mill ash, improve soil structure, nutrient availability, and water retention while counteracting acidification. These amendments also reshape soil microbial communities, enriching beneficial taxa, suppressing pathogens, and increasing network stability, alongside functional shifts in N fixation, P and K solubilization, mycorrhizal symbioses, and plant growth promotion. Enhanced enzyme activities and functional microbial abundance drive improved C, N, and P cycling. Based on site-specific long-term trials, sugarcane industry by-products can replace 25–50% of inorganic fertilizer under conditions where environmental risks are appropriately managed. Future research should prioritize region-specific amendment strategies, precision agriculture tools, functional microbial characterization, standardized soil health indicators, and socioeconomic assessments of adoption constraints. This review provides a framework for transitioning to soil health-centric nutrient management, with implications for China’s sugar security and sustainable agriculture in Yunnan’s diverse landscapes and beyond.