Background and aims <p>Continuous chemical fertilization is threatening acid soil sustainable use because of soil acidification aggravation and microbial function destruction, whereas organic fertilization has the potential to overcome these shortcomings. However, the mechanisms underlying sustainable crop production under organic fertilization in acid soils are largely unknown. A multi-omics approach provides the opportunity for a comprehensive and deep understanding of how organic fertilization sustains acid soil productivity.</p> Methods <p>We examined maize yield, mineral nutrition, leaf transcriptome and metabolome, rhizosphere microbiome, and soil fertility in a 25-year acid soil field trial including four fertilization treatments: a control without fertilizer, chemical fertilizer, organic fertilizer, and combined chemical and organic fertilizers.</p> Results <p>This long-term fertilizer trial revealed that applying organic fertilizer sustained high maize yields over 25&#xa0;years compared with chemical fertilizer. Organic fertilization improved soil fertility and maize mineral nutrition especially phosphorus by enhancing the cooperation between the rhizosphere microbiome and the maize transcriptome and metabolome. Identified microbial keystone taxa, plant functional genes, and metabolites differing between organic and chemical fertilizers were mostly associated with the phosphorus cycle, suggesting that phosphorus is a major contributor to sustained high productivity resulting from organic fertilization.</p> Conclusion <p>Organic fertilization sustains high maize yields in acid soils through the cooperation of rhizosphere microbes and plants. Phosphorus is the key contributor to acid soil sustainable use under organic fertilization. These findings have important implications for optimizing fertilization regimes in acid soils, ultimately contributing to food security and agricultural sustainability.</p>