<p>Biochar is increasingly recognized for its capacity to remediate acidifying soils, but the mechanisms through which it achieves long-term effects remain poorly understood. This five-year field study examined how biochar’s effects on soil chemistry propagate through biological systems to reshape soil function. We conducted a randomized field experiment comparing three biochar application rates (4.5, 11.25, and 22.5 t ha^–1) with lime and swine manure in an acidic paddy soil. Integrated soil microbiome, metagenomic, metaviromic, and metabolomic analyses assessed how amendments altered soil properties and their associations with microbial communities and metabolic functions. All amendments alleviated acidification (pH increased from 5.5 to 6.4) and reduced exchangeable aluminum (from 12.5 to 3.5&#xa0;mg&#xa0;kg^–1). High-dose biochar (22.5 t ha⁻¹) initiated a mechanistic cascade absent under traditional amendments: improved soil chemistry drove restructuring of prokaryotic and viral communities toward nutrient-cycling phenotypes (enriching Chloroflexi, Planctomycetota, Algavirales, and Crassvirales), which in turn reshaped metagenomic functions and soil metabolite profiles. Specifically, biochar elevated genes related to nutrient exchange and cell–cell interactions while enriching lipids and terpenoids that support plant growth and long-term carbon stabilization. This coordinated restructuring of soil chemistry, microbial communities, and metabolic function did not occur under lime or manure. The findings demonstrate that biochar’s long-term superiority emerges from orchestrating sequential changes across the soil-microbe-metabolite system as an integrated whole. This mechanistic understanding provides novel insights for deploying biochar as an ecosystem restoration tool in acidifying agricultural systems.</p> Graphical Abstract <p></p>