Background and aims <p>Ecological stoichiometry provides critical insights into plant physiological strategies and nutrient cycling, yet how soil amendments influence crop yield via organ-specific stoichiometric traits remains poorly understood. Here, we aimed to disentangle these mechanisms with contrasting amendments.</p> Methods <p>A field experiment was conducted, with four treatments: control, straw return, biochar application, and silicon-modified biochar (Si-biochar) application. During two rice-growing seasons, we measured rice yield, growth traits, soil parameters, and organ C–N–P concentrations, allocation, and mass-based C:N:P ratios. To distinguish biomass-driven dilution/concentration effects from C-N-P uptake changes, we developed a novel Elemental Concentration Change Attribution Index (ECCAI).</p> Results <p>Straw return reduced yield by 22.7%, whereas biochar and Si-biochar addition increased yield by 26.8–28.2%; similar patterns emerged for biomass, root length, and chlorophyll content. Soil amendments influenced C-N-P concentrations, stoichiometric ratios, and their partitioning among organs. ECCAI showed that under biochar or Si-biochar treatments, whole-plant C-N-P concentrations were primarily driven by enhanced C-N-P uptake, whereas straw return induced shifts through biomass concentration together with altered C-N-P uptake. Random forest analysis identified organ-specific stoichiometric traits, including leaf N concentration and C:N ratio, as the main predictors of yield in both early and late rice. Structural equation modeling indicated that amendments initially modified key organ-specific stoichiometric traits by influencing soil properties, which subsequently affected growth traits and ultimately yield.</p> Conclusion <p>Soil amendments alter rice yield, and these yield responses are associated with changes in organ-specific stoichiometric traits, particularly leaf N concentration, providing a stoichiometric framework linking soil amendments to crop productivity.</p>